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999s Restoration & Rebuild

18213 Views 97 Replies 15 Participants Last post by  edgar999s
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Hi all, and welcome to curious visitors from Chromeheads also ;)

Thought I'd share my restoration work on the 999s. Once hailed as the 'ugly duckling', many buyers are now waking up to its timeless design. I was one of them, receiving this 2003 model with 987km in June 2020. I had little to no information to go on other than photos and the seller's word, and unfortunately the bike turned out to be a lemon, though not entirely the seller's fault - he probably just didn't know any better. I had hoped it was in good condition on the basis of the very low mileage, but that wasn't the case. Was a lot of back and forth on that sale.. Anyway, long story short, I eventually stuck with it and got a partial amount of my money back, allowing me to move forward.

Here's how she looked online -
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Day of loading up for her journey -
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And arrived 3 days later -
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Bike was known to not start. While I wasn't looking to mod or enhance it in any way, it did need a lot of my attention. Here were the early stages of me diving in, slowly opening up the can of worms. End of diagnostics concluded -

  • dead battery
  • rusted spark plugs
  • rusted vertical cylinder spark plug tunnel
  • rusted horizontal cylinder intake valve + seat
  • badly rusted fuel tank
  • ruined fuel pump
  • clogged injectors
  • worn + rusted clutch disks, basked chewed, fractured spider spring
  • evidence of crash on left side
  • spoiled oil cooler
  • degraded sound dampening material
  • leaking fork seals
  • expired stator unit
  • aged upholstery + worn rubber components
  • scratched/broken bodywork and carbon fibre components
  • bent rear brake lever bolt
  • once engine was running, coolant was found to be mixing into the oil - bad vertical head gasket

Other areas to address -

  • air filters
  • oil + coolant change
  • timing belts
  • brake + clutch bleed
  • chain + sprocket set
  • brake pads
  • tyres
  • valve adjustment
  • upgraded earth + starter wiring
  • exhaust manifold ceramic coat

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Oil drain plug magnet, not too bad -
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Thank you Johnny, I'm fighting with all I have left in me 😄. Honestly there have been entire bike shops that have turned me away because they don't want to deal with this bike. But I get that, I get that they prefer to keep bikes moving in and out quickly. These forums, the Facebook group and a few bike enthusiast friends are all I have. You explain things very easily and I'm glad you wrote in. I'll reply to you down below. Where I'm at now -

The new battery arrived after a long wait and the bike was back together, ready for go time. This is THE most powerful battery I could find that could fit within the space provided. A 330CCA and 14Ah hybrid powerhouse from Motobatt that according to them combines the best features of AGM and Lithium -
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Aaaaand unfortunately there was no go time. Zip. Nada. Zilch. Battery would show 13.2V on the multimeter and 12.6V on the dash, which was fine. Bike would crank well the first time but not start, then do a two-crank-dead thing for all subsequent start attempts. Stumped yet again... At one point I noticed that the oil light would flicker as I worked the shifter - come to find out I had crossed the receiving connectors for the neutral switch and the oil pressure. Simple mistake, hope someone out there learns from me. Oil pressure is white/yellow on the harness and neutral is green/yellow -
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Convinced that this was the last piece of the puzzle, I cranked and cranked, trying different secondary ground arrangements, spark plugs, TPS resets, booster batteries and startup-spray. Nothing really worked. The most I could get was a bumbly rev for a few seconds with the startup-spray. Unfortunately, the dreaded intermittent injector spray and spark were back in full force... :confused: This points to the problem being not with the start but the general running of the engine. I find it very frustrating that I got it going in prior instances and now it wouldn't run again. Moving goalposts, as they say, for days on end. So I put up a few videos on Facebook and the suggestions came in that it could be fuel pressure related, a bad starter, valve adjustment, timing belt misalignment, TPS setting, not enough open throttle at startup, not enough battery power or a bad crank position sensor.

The point that Johnny makes about the contact between the head and the crank case is true - during the engine work I applied liberal amounts of rubberised gasket maker around the existing metal gasket which could weaken the ground. So I tried the additional ground from negative directly to multiple points on the frame but hey ho, no luck. Bike continued to sputter and die. I also tried a secondary ground for the ECU. It was most definitely worth a shot though, and I'll take all the support I can get. What I think is that even though the rubberised gasket could weaken the ground, there are still four main cylinder studs which run through the head and fasten it directly to the main engine body. My main ground looks like this -
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Having ticked most suggestions, the one thing that I have a hunch on is the crank position sensor. It's something that I tested but still have my suspicions. Someone mentioned that even though theirs tested out ok they still had it replaced and their bike ran afterwards. It's a generic Fiat part so it's not a big investment at this stage. I'm just weary of buying into a new ECU/wiring harness as I'm way over budget already with this project. The one other purchase I could accept was a set of Champion RG4HC spark plugs which are stock for this bike. The old Champion plug I had (the one that wasn't horrendously rusted), seemed to produce a slightly better spark than the new NGK CR9EB. Again, worth a shot and not a big investment. Hey, whatever little bit can help the bike along. If neither of those options work, I'll go back to the fuel pressure regulator.

These items are small and available within the country, so should arrive next week. While I wait, at least I have something nice to look at. She may be a dead horse, but she's a pretty dead horse :)
Tire Wheel Fuel tank Automotive fuel system Automotive tire



As always, all suggestions, comments and ideas welcome!
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Hi Edgar, sorry to hear no go yet. You state that you added grounds from the battery to the frame. What I am suggesting is a single wire (6 mm diam.) from the starter motor to the negative terminal of the battery.

When you replaced the starter motor, you had one bolt covered by the alternator case and two bolts exposed (the 3 bolts fixing the starter to the block). I am saying to attach the ground from one of the two exposed bolts directly to the battery ground (not the frame).

By adding grounds from the battery to the frame as you have, the circuit still has to pass through to the head and that existing, factory ground wire, you need to bypass that factory ground wire, so when you hit the starter, you have a complete, un-hindered circuit from the battery to the starter back to the battery.

Without resistance (ie stock from the factory brand new) a standard 190CCA battery is fine, so with that battery you now have to not even trouble the issue is simply confirmation to me, that your issue is one of grounding. The bike doesn't start.

Another confirmation is the 2-crank cut-out is still present. So the ECU is detecting a drop in voltage under 9.5 (there abouts) and cuts the attempt to save the battery. 13+ volts in the battery and 12.6 at the dash then becomes less than 9.5 due to one reason...a short/open circuit, most commonly, bad grounding.

Whilst other issues such as bad plugs, injectors, CPS's etc would present more as poor running, the bike would still start in most of those cases, the fact it doesn't start suggests a grounding issue.

Another thing to check with the CPS is the air gap. Again, I have played with this and the bike still starts, it may be harder, but still starts (until you are way off). What it does impact is the running and especially the idle.

Sorry to sound like a pest, but you are so close, I can feel it :):)

Cheers :)
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Hi Johnny,


Thank you once again. I know I'm close. It's like I just need one last piece to complete this giant puzzle. I did a temporary fit of a 6mm wire as instructed as per images below. Would you say this is ok (the copper is clamped down by the washers), because there was unfortunately no change/improvement -
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Some other things - that isn't the factory ground wire. That's a 10mm upgrade I did a while back, which was applied to the entire starting circuit (positive to solenoid, solenoid to starter).
Two-crank-dead symptom was cured when the crossed wires for the oil pressure sensor and the neutral sensor were put correctly.

New CPS just arrived :) but I'm very put off by how the clearance is to be checked - the entire radiator and coolant manifold have to come off!!!! Bad design, Ducati. Bad bad design.

Champion plugs are still on the way, and I still have my suspicions about the fuel pump.


We're in this together. Onwards, to glory!!!
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Hi Edgar,

Even if it's only a test set-up, it would fix the issue if that was the problem so it obviously isn't the problem. At least you tried and ruled that out!

With the CPS, you don't have to remove everything, when I replaced mine, I removed the battery tray and the single coolant hose with the water pump housing. Still a pain to replace a sensor but no need to remove the manifold or radiator, just drain the fluid into a clean bucket and re-use. You can either get the factory gasket for the pump cover or 3bond works just fine (with 20k+ and no leak, I can attest to that).

Keep up the fight!

Cheers :)
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Thanks Johnny. Yeah she can be a real pain, right? Every time it's like that for me. Every time I think I've found the issue.. Blam! bike gives me the finger :LOL: Five months of this crap now. I don't mind so much changing the CPS, it's just the way the clearance is to be checked...

So an update - Champion plugs arrived. Installed along with the new CPS -
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Aaaaand big surprise, she still won't start :cautious::cautious::cautious::cautious:

Bought a fuel pressure testing kit. Seem to be getting only 2 bars of pressure. Should be 3. Could this be the final piece of the puzzle then??? Stay tuned to find out....
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So as mentioned, I was only pushing 2 bars of fuel down the line. Should be 3 -
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Swapped out the old pressure regulator again for the new one and saw a healthy 3 bar on the gauge. Got all excited, and blam!! Bike gave me the finger again...

I really thought I had it.. Nope. Still lousy, sporadic injector pulses. Still sputters alive with starter spray then dies. At least I got some clarity on the fuel pressure thing - the old regulator seemed to work but would get stuck at 2 bar. The new one is factory set to 3.2 bar, and the pump itself is set to push 3.8 bar. So the first time when I put in that new regulator and saw the fuel squirting out the top I thought it was jacked, but it wasn't. That was the remaining 0.6 bar being allowed back into the tank. I think that's how it works, right?

So now, I guess I could dig in and check the CPS air gap? What say you, Johnny? I'm shooting in the dark again. Btw what genius thought to put the inspection access there -
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I have a spare ecu if you know anyone who can disable the immobilizer.was a spare when I bought the 999s '04.don't know if its compatible but maybe it can be re programmed.you pay postage.thanks for sharing your adventure-injector misbehaving could be the ecu.
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I have a spare ecu if you know anyone who can disable the immobilizer.was a spare when I bought the 999s '04.don't know if its compatible but maybe it can be re programmed.you pay postage.thanks for sharing your adventure-injector misbehaving could be the ecu.
Why yes sir that would be sooo helpful I'll take you up on that offer thank you! Will PM you.
So as mentioned, I was only pushing 2 bars of fuel down the line. Should be 3 -
View attachment 172783

Swapped out the old pressure regulator again for the new one and saw a healthy 3 bar on the gauge. Got all excited, and blam!! Bike gave me the finger again...

I really thought I had it.. Nope. Still lousy, sporadic injector pulses. Still sputters alive with starter spray then dies. At least I got some clarity on the fuel pressure thing - the old regulator seemed to work but would get stuck at 2 bar. The new one is factory set to 3.2 bar, and the pump itself is set to push 3.8 bar. So the first time when I put in that new regulator and saw the fuel squirting out the top I thought it was jacked, but it wasn't. That was the remaining 0.6 bar being allowed back into the tank. I think that's how it works, right?

So now, I guess I could dig in and check the CPS air gap? What say you, Johnny? I'm shooting in the dark again. Btw what genius thought to put the inspection access there -
View attachment 172784
Hi Edgar, the existing CPS should have had a shim between it and the casing. From the factory, you can purchase 3 different thicknesses to account for any changes / modifications to the crank flywheel and / or sensor itself.

I would simply replace the CPS with the existing shim as you haven't changed the crank flywheel and I am assuming the new CPS is the same length as the old.

I got the other 2 shims to play with and they made no difference until I added a washer (for curiosity sake) and the bike would not start. I also removed the shim altogether and it worked fine (the issue would be if there is not enough clearance between the crank flywheel and the CPS tip....).

Bummer the bike still won't start but it will eventually and when it does, you will know the ins and outs of your baby and there won't be anything you can't fix on her going forward....experience, a true friend for life!

Cheers :)
Thanks Johnny. I'm right there with you on the shim. I pulled the manifold and radiator to get the feeler gauge in there and my clearance was only 0.5mm. Book calls for 0.75-0.95mm. Had a custom size shim cut from some plate and it worked perfectly. Clearance now at 0.85mm -
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Still no start unfortunately, but it's ok. A user who I know as 2004 999s has send over his spare ECU, for which I'm truly grateful. Thank you sir. While waiting, want to knock a few more things off the list -

1. disconnect injector connectors, load the fuel pump and tap the terminals a few times with a 9V battery.
2. open air bypass screws on the throttlebodies, currently at 1.5 turns out
3. not feeling up to it but I can pull the harness and install new wire for injectors, and at the airbox
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Everything you do is getting you closer, so keep up the good work Edgar!

Cleaning the injectors is a good idea and easy to do. The air bypass is plenty out at 1.5 turns so I would (at this stage) leave them be, again, it would impact running but would have to be grossly wrong to prevent starting.

Leave the loom until after you have tried the replacement ECU, if it's the ECU, you'll save yourself some angst!

Cheers :)
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Hi all,


Back with an update on things, and I'm happy to finally have some good news!

I am still to receive the replacement 999s ECU in the mail, but to the member who sent it, I thank you once again and will be sure to return it as soon as it arrives. You have my word.

I worked through the 3 options listed above as my impatience had got the better of me, but didn't have much success with the first two. Zapping the injectors would just load up the throttlebodies with fuel and I'd get a brief cough and sputter. Much like the starter spray effect. Playing with the air bypasses also didn't yield much. At one point I even tried a jump start from a Toyota Hilux with no luck. So I bit the bullet and pulled the harness back out.. Sometimes, it's quite hard to admit to yourself that you didn't do something right. I tend to assume that once I've addressed something that that's it, it's fixed. But sometimes you just have to swallow your pride and go back in. Turns out that after the first loom overhaul, some of the pulling and twisting that naturally goes on as you fit it into place had caused two connections to come loose internally. And one of them was specifically to do with the injector relay.

And so, that was the last piece of the puzzle :giggle: I put everything back together and she started up. Healthy idle at 1250rpm. Minor tweaks and balances made with the help of a vacuum gauge the next day, and that was it!

Her first test ride -
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Very well behaved and responsive. I had a minor niggle where I didn't use thread locker on the clutch spring bolts and the things wound themselves undone. I felt it as the bite point gradually moved further away up the lever's travel, until almost gone entirely. Was lucky to limp home but an easy fix otherwise. Ceramic coat on the exhaust holding up well and no other major issues.

All dressed up and on the road for her first outing :) -
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So that completes my journey. I'd like to thank everyone on this forum for your support, input, motivation and compliments. You all kept me going. Thank you to everyone on the FB group, my bike enthusiast friends, to MP Custom Valve for the Ohlins service, Gary who helped with the paint job, Frank for the exhaust work, and Chris for the seat upholstery. All the parts centres around the world that shipped what I needed, and thanks to my friends and family.

For those wondering, I'll put up some numbers -

Project started mid-June 2020, ended early Nov 2021

Bike delivery - $213
Raw purchase cost of bike - $4,050
Admin/registration - $272
Parts, tools, paints etc. - $4,960
Total shipping/customs fees - $1,060

Lump sum cost of project - $10,555

Dollar/Rand conversion $1:R15.57 (18 Nov 2021)

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Tire Wheel Fuel tank Automotive fuel system Vehicle



Yeah, it's been one hell of a journey. She was crying out for a doctor and somehow I heard her.

Thank you all!!!


Edgar
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Edgar, congratulations and you are a man among men for pushing through to the finish line on this project. Love seeing this bike back on the road and hope you get lots of seat time to compensate for all the hard work you put in. Congrats again!
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This is truly inspirational.

Most people would have given up months ago.

Out-freaking-standing. This thread deserves to be a sticky at the top so everyone can see it.

Who's an @admin here?
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@edgar999s - Thanks for inspiring me to get on with my 999s build! I've had this bike for 18 months now and it's just been residing in a corner of the garage, but after watching your build it's inspired me to get off my arse and get this thing started. Not wanting to hijack the thread but now that yours is completed I thought this would make a logical addition to what you've started

Purchased ex-Japan this is how the bike looked on arrival.
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So far I've completely dissasembled the bike as I'm changing the colour to red not being a big fan of yellow.
:)
Belts have been done plus a few minor oil leaks fixed (bike had done less than 18,000km) wiring loom overhauled and re-wrapped with HellermannTyton Cloth Tape which has tidied up the sticky black mess that the loom was! Headlight shell, fairing stays and sidestand repainted and headlights upgraded to LED along with the 'both lights on in high' mod.
Frame and bodywork has come back from painting (just waiting on some OEM side fairings) and shock, forks and steering damper overhauled and resprung/revalved. So it's down to the slow work of reassembly....
Will post some more pics as progress continues.
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@cs363 woohoo go for it my man!! I'm keen to see 😊
ed, that was an amazing resto, and you should be very proud. i loved those 999's. i had a black 05 S that i wished i kept.
great job!
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Here's some pics of the bike in dissasembly mode...

Crusty wiring loom:
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Engine out, cleaned and awaiting some new gaskets etc., note 'trick' factory engine stand...:

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In pieces (new tyres were fitted prior to tear down in order to complete certification/registration)

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Hellz yeah man keep it going! You're at a very high level of workmanship I can see that clearly 👍
Well....a pleasant surprise lurking under the clutch cover.... 😁

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