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49 Posts
Discussion Starter · #1 · (Edited)
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 -



Day of loading up for her journey -

And arrived 3 days later -

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




Oil drain plug magnet, not too bad -

49 Posts
Discussion Starter · #2 · (Edited)
State of the fuel which I drained out into a pot. I cannot express to you how much this stuff stank. My entire house reeked for about 4 days -

Fuel tank interior -


Degraded oil cooler -

Juicy spark plugs. They look amazing -

Glorious fuel pump -

Slowly working my way through the first phase teardown (the one needed to just get the engine running) -


Sad state of the sound dampening material -


49 Posts
Discussion Starter · #3 · (Edited)
Tank soaked in vinegar for 3 days. Then drained and air dried. This is the rust that came out afterwards... -

Then, in with a scrubbing brush and water. Over and over until only clean water ran out -

Fuel pump also vinegar soaked -

Looks a lot better but the pump was still dead -

Back to the fuel pump for a complete repair this time -



DIY injector clean -


New plugs arrived -

49 Posts
Discussion Starter · #4 ·
And oil + coolant change. Hoping for an engine start -

Lithium attached for maximum cranking power, but dang, no luck... -

At this point I came across the rusted valve. Not much I could do about it yet, it would have to be addressed during the engine teardown -


With a bit of further reading, I isolate and address the wiring issues -


And she fired up strong!! Damn what a sound. What an absolutely sensational sound. I took her for a quick lap around the neighbourhood to feel for any other issues -

At this point I noticed the coolant-to-oil breach and poor clutch. Clutch inspection came out as follows -



49 Posts
Discussion Starter · #5 ·
At least the first phase I was happy with. She ran. She did have some of the cutting out issues that needed to be addressed with the TPS reset, idle adjustment and TB balance in conjunction with the exhaust gases, but I'll do that after the second phase - which is the total teardown and restoration. So, diving back in -


Ohlins goodies off for complete overhaul -

The bike came with stock and race fairings. I took the stock fairings to a vehicle centre for paint and am selling the race fairings. Scratches like this were prominent throughout -


Guys helping me fight the good fight. I fed them one or two parts at a time until we ran through everything -

A thousand times better -

They had a go at some other components as well, like the swingarm -

And the carbon fibre accessories were refreshed with lacquers from a place that makes kayaks -

Getting deep into it now -

49 Posts
Discussion Starter · #6 ·
This is a familiar sight in my kitchen. Engine on the counter... -

Stator definitely needs replacing -

Engine cleaned, valves, pistons, gaskets etc. -





One happy engine. Still needs new timing belts and valve adjustment - waiting on parts to arrive -

And on to reassembly -

Most definitely a two-man job. No doubt -

49 Posts
Discussion Starter · #7 · (Edited)
Some more parts coming on - swingarm, airbox and muffler. All torqued to spec with new stainless steel bolts and copper anti-seize -
Machine Auto part Engine Technology Automotive engine part

I had a go at painting some odd parts here and there myself, like the rear wheel adjusters and sprocket carrier -

Parts cleaned, restored, and waiting -


Wheels cleaned, new rotor bolts, bearings inspected ok. Tyres fitted and balanced - Diablo Rosso 3's, 120/70/17 front, 190/50/17 rear -

Rear fitted and happy. DID 525 ZVMX with 98 links, JT Sprockets 15/38 -

New pads arrived -

And her very own lithium that fits -

Seat back from upholstery -

She's looking good! People often ask how I suspend my bikes - I hang them off my roof trusses :LOL:

49 Posts
Discussion Starter · #8 · (Edited)
Ohlins goodies arrived back, so with that, I was able to sit her back down -

New stator arrived and installed. Will have to see how it co-operates with the Lithium -

So that's where I'm currently at. Any new work will come up in future posts. Still a bunch of stuff to address but it's coming along nicely!

All thoughts, comments and suggestions welcome :):)

49 Posts
Discussion Starter · #13 ·
Great photos. And some excellent work! Wife would kill me in 2 seconds flat if she saw that in the living room.. ;-) I look forward to seeing more photos and reading of your progress.
Haha. Thank you! Assert your dominance in the house. Caveman style.

I expect parts to start arriving soon so hopefully we can get back into progress with this fine girl.

49 Posts
Discussion Starter · #14 ·
Hi all,

Small update here as some parts have trickled in. I got these Flennor belts which turns out have a bit of a bad reputation... Will see how they get on. These will be fitted in conjunction with the valve adjustment once I get the shim kit -

Some other small items -

Bike's current state. She's very patient with me...

Catch up again in the next one!

49 Posts
Discussion Starter · #18 ·
Thank you! Man I literally have no idea what I'm doing :LOL: This is only the second bike I've ever worked on. But I guess I do have good hands, I got that from my dad. I enjoyed taking it apart, especially the engine. It's like a feeling of exploration. Most important thing is to just read extensively and watch others do it. You gotta make the service manual your bible.

49 Posts
Discussion Starter · #20 · (Edited)
Hi all,

Things have been ticking along and parts are rolling in slowly but surely.

A big milestone covered was the completion of the Cerakote on the exhaust. The previous tub I bought was incorrect so had to re-order. End result as follows -


Automotive lighting Motorcycle Automotive tire Motor vehicle Fuel tank


With that, I could then finally get the new oil cooler on -

Valve shim kit arrived from the States -

But shortly after getting into the valve adjust, I found a fractured half-ring... :( Very strange how that happened.. When I had the engine apart in the kitchen, all half-rings were fine and intact. The engine wasn't run or anything since then and now, except the odd hand turn here and there. Oh well.. I've ordered replacements, plus a few other ancillaries.

The long-awaited clutch also arrived. Installed all good. The unit is now an amalgamation of Sigma Performance and Ducabike components -



Keep the comments and suggestions coming folks! It helps me keep going.

49 Posts
Discussion Starter · #22 ·
The cerakote on the pipes looks great. Great progress, how much longer do you estimate for completion?
Thank you!! The half-ring replacement should come in next week so I can get on to the really big and exciting one, I'd say by end of the month - the engine start! After that, engine fine-tuning, test ride, then fairings on and she's done.

I've also been trying to connect up to the ECU via the VAG-COM cable, Fiat adapter and the JPdiag software, but haven't had a successful connection. I'm trying to get the JPdiag software unlocked to do the TPS reset. My preliminary guess is I'm using the wrong Windows version. Does anyone have any experience in that area??

49 Posts
Discussion Starter · #25 ·
Hi all,

Thank you Abnmike, those are kind words and I may be back in the States again soon so might take you up on that offer!

Edufox, thank you too! You look a lot like me in your profile pic, haha. Callipers are just as clean on the inside as they are on the outside! They were very fouled and it took days and days. I usually work with a damp microfibre cloth wrapped around the tip of a flat screwdriver - a normal sized screwdriver for regular cleaning and a long thin one for hard to reach areas. After that I'll hit all areas with Autosol polish with the same cloth, and lastly I'll finish off with a clean dry cloth. Yeah it's a long process. I tend to approach the restoration as "chipping away" until all is complete. I love breathing life into her and seeing the result.

Here's a quick update -

Half-rings arrived, so I could get on with the valve adjustment. Was a two-day affair. I actually came across another 3 fractured half-rings (!!) -

Radiator on and filled -

Flennor belts in and tensioned -

This was a screenshot from a video recording. She fired up and revs well, but cuts out and will not idle. It was as expected. I desperately needed to hook the laptop up to her, but as it turned out I had a bad VAG-COM cable which was causing the connection failure. So with that, I'm awaiting the replacement cable from the supplier and hoping the next update will be promising!

Until then, all comments and suggestions welcome!

49 Posts
Discussion Starter · #27 · (Edited)
Ola' amigos and compadres,

Thank you for your words of encouragement. It's been quite a rough process of trying to get this thing going. I wish I could say I've got a running bike now, but I feel I've hit the limits of my capabilities. The bike is incredibly temperamental and seems to exhibit changing symptoms, which makes it very difficult to pinpoint what the problem is. Like troubleshooting a constantly shifting target. A brief summary -

Played back and forth for several days trying to get a successful connection to the ECU. Eventually came right with the WCH chipset with pins 4 and 5 soldered together, using the drivers that came with the CD and running from Port 4 (other ports don't seem to work for some reason). Fiat cable test all correct and successful.

JPDiag software had the TPS and Service reset buttons available - no need to register/unlock anything, so that was nice, I guess. Maybe JP was tired of getting emailed constantly so he just put the software out there in full. Software responsiveness was ok initially but became very poor - sensory feedback seemed to deteriorate as time went on. By the end of the evening I'd get a successful connection and then no further response from any of the measured parameters. Played with port settings - nothing. Hoped and prayed.

Next day, got enough of an "open window" stable connection to squeeze in a TPS reset quickly. Did the double-reset procedure at 2.3 degrees as according to BradtheBikeBoy. Hooked up a home-made vacuum gauge, then wound the bypasses in and worked them back out equally 1/4 turn at a time. No notable positive effect on the idle. Bike still stuttered and stalled almost instantly, until I'd run the battery dry and have to leave it.

More recent attempts to start the engine have been really perplexing. The bike's condition seems to have become increasingly unpredictable and unstable. I'd lose spark on one attempt, then lose injector spray on another. They'd come back sporadically, bike would be able to rev once and then die out again. Then not turn at all. Then turn a little bit. Then turn without injector spray. Just a total mess. The fuel pump does buzz on each key on. Checked and double checked all wiring, grounds, fuses and connections. Replaced new spark plugs with new new spark plugs. Potentially may have hurt the battery from all the cranking as it's taking very long to charge up to full now. Also don't want to crank excessively and wear out the sprag...

I'm beginning to think the ECU itself is problematic. Somehow, between the perfectly fine test ride last year and now, something has failed somewhere. I've spoken to a few guys and I think the best way forward is to load the bike up and take it to the dealership. It's 1000km away but it has to be done. As I say, it's simply beyond my capability to work out what's wrong at this stage. If anyone has any suggestions/ideas, I'm all ears!!



49 Posts
Discussion Starter · #28 ·
Haven't loaded the bike up just yet. I bought and put in a new fuel pump/coil relay today. Still same symptoms. Gonna check out the fuel pump and crank position sensor. Goddamn it! Help me step bros, I'm stuuuuuuckkk!! 😩😩

49 Posts
Discussion Starter · #29 ·
Well, after an entire day of testing, diagnostics and scouring through the forums, I've finally found the issue - part of the fuel pump assembly was still old and problematic. Specifically, some of the wiring and the pressure regulator. Surprisingly, the wiring passing through the bottom flange was fine (known to fail), but in other places it was lousy. My pump repair last year maybe could have been a bit more thorough!!

I get why it was so difficult to diagnose the issue - there was a compounding effect of low fuel pressure, electrical fault and throttlebody work needing to be done, all happening at once. In medical terms, "comorbidity". I'm just glad I got through it. I was about to throw in the towel and take her up to the dealership. I had her prepped and everything!

So, new pressure regulator is ordered and on the way. Also, this thing was completely deteriorated and I need to replace it before I can move on. Pulled this image off Google. Am I right to say it's the low fuel level sensor? Or?? Anyone know what it is? -


49 Posts
Discussion Starter · #31 ·
A friend in Spain!! Dude I was meant to fly up there June last year for the Mad Cool music festival to see my favourite band and go run with the bulls. Stupid Covid ruined everything! Festival got postponed to 2022 :(

Thank you! I'll post an update once the fuel pump is properly repaired, and then I'm beyond positive she will fire up!!
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