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I was recently going through this similar issue on my recently purchased low mileage 1098s. Rough idle, would stall when engine was warmed up, exhaust was soooo hot my nuts would be roasted at the end of a ride, I also found it difficult to find the clutch point and it would always look and sound like I was still learning to get off the mark in 1st gear.
I resolved my issue as follows.
Rough idle, stalling - grabbed myself JPDiag software and updated the ecu with 96518507B map (known issue with '07 stalling with original map 96518607B) Ducati Aus resolved it with the update ECU software which I obtain via JPDiag writer software. Ran much better on idle, however still would stall, although less often.
Stalling, clutch - finally resolved this with a number of issues found. Resetting the TPS with JPDiag wasnt sorting the issue. I then found the throttle cable was sticking a little and discovered that the lock nut adjusters were damn loose. Readjusted the throttle and it was like night and day. No more stalling and clutch point was perfect.
Stalling - it started to stall on me again a week later and then the fuel cap started to pop... WTF, I found that the venting tubes were blocked which would have created counter pressures for to fuel injection pump (Unable to fill with air when pumping and expanding when not riding. It was odd though, as it was popping while I was riding. Anyhow, Cleaned them out, now happy days....
 

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PS, who, when was the timing belt done?
My last resolution is to double check the timing belt as it feels like the timing is a little retarded. When i changed the belt I didn't have the tool to hold the cams and when you tighten the tensioner pulley, the cam gears move with the belt. I'm fairly sure this also played or is playing a part in my running issues.
Once the cam holder tool arrives, I'll be redoing the belts properly. That is, backing off the nuts that hold the cam sprockets on the cam shafts, wile the shafts are held in place. Tighten belt, cam sprockets will move a little, but cam is held at the correct timing. Then retighten sprockets once belt is tensioned.
 

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Lastly, yeah. My crank sensor was throwing error codes too. Replaced with new and all good when I did the throttle cable adjustment.
This is all just arm chair mechanicing too. Hopefully we arent sending you down the garden path on wild goose chases.
The way you check for spark seems good to me (I would have done the same) so I believe your getting spark. My 2 cents worth is that you may have skipped a tooth on the timing belt. If you haven't already determined which cyclinder isnt working. (sounds like you have) Remove the coil from one and turn over, then same with the other cylinder. Which ever cylinder has coil on and you dont get ignition (but theres spark) check the timing for that cylinder.
 

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If you could get it hooked up to a diagnostic, it will show up any registered trouble codes. I'm assuming your dash cluster hasn't thrown up any errors here.

What does the dash read when you first turn the key? 1098 RACING? This will give an indication of the map installed. The updated ecu reads 1098 RACING EVO which came in from '08 on. My original map read the same sans the EVO. When I had a look at the fuel mapping of the original map it looked like a dogs breakfast. I was amazed it even ran.
Yes I agree that there could be some flash from the fuel, but that's dependant also on air fuel mixture. If valves aren't timed right, that ratio will be effected. No amount of good spark will ignited a flooded chamber. For combustion you need 3 elements. Heat, fuel and air and these need to be at the right ratio for ignition to occur. I guess, double check connection, test coil resistance, hey see what happens if you swap the coils. Does the problem shift to the horizontal cylinder?

Feel your pain mate, I was tearing my hair out during my diagnosis.

I'm still leaning towards checking the timing belt, which most owners can do at home.
It's not intended as a slight against whomever last changed the belts either. Shit happens through no fault of anyone, bad belt, tensioner issues, etc.
 

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Yep, so you should have the updated mapping with the 'EVO' on the dash and you could certainly say you have ruled out a coil issue. I would think a coil failure would also throw an error onto your dash anyway. You should be able to tell by the notches on the cam shafts. At TDC, the horizontal notch should both be level with the top of the head and the tail notch (if you think of it as an upside down T) pointing away from the cylinder.
It sounds like your hands on too, I'd take a look at the timing, not overly difficult to do. If anything to at least rule that out. But ..... my $$$ is on timing at this stage.
Are you happy that the throttle cable hasn't loosened off or in need of adjustment?
Mine were loose and there'd be just a little further movement of the butterfly to the closed position beyond what the throttle grip would close. As such, on engine start up, for some reason the TPS would lower (I suspect the air suction) and effectively give a lower idle along with the damn stalling issue. Just a thought.
 

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Sorry mate that last post was a little disjointed and can't seem to edit it Fromm the phone. I meant to say that I would still check out your timing, if anything just to rule it out. It's fairly easy to do ... and then I go off and describe the notches inbred cam shafts.
 

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Don't forget the belt tension too. You should find it takes some effort to twist the belt beyond 45 degrees at its longest length, if you aren't able to test sound resonance, although you can do sound test easily with your mobile and any number of free apps.
 

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You know if you flick the mode button up it will give you what error codes are being indicated? If there's more than one they will scroll through.
Possible errors with standard ecu - are your lambdas connected, is your exhaust evap valve connected? These are normally removed with a full exhaust system, hence the need for the change in ecu.
 

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While you have the right fairing off, it's less labour to check the timing than replacing the old bits back on? Just saying. Whatever it is, hope it's sorted soon for ya mate. Sucks having the bike off the road.
 

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Well, error code 38 is indeed the CAN line error. The usual suspect for this error is the ground connector to the body of the ECU, loose, corroded, wire broken/fracturing along its length at some point or otherwise the ECU body isn't being grounded. A second suspect could be corrosion of grime effecting contact between the ECU pins and its respective connector. Check and clean both ECU and connector pins. Otherwise wiring harness may be fuked somewhere?

Mate, you sure are having a time of it... Not wanting to state the obvious, however for the sake of any new readers or owners researching, make sure that any electrical work is preceded by disconnecting the battery first and foremost.

As Dutchie intimated, the immobilizer function is married to the dash/instrument cluster. If the dash recognizes the key, it gives the ECU permission to fire away. If the dash is changed, keys need to be programmed to it (unless a new set came with it).
 

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Back to your initial probs, could the connector be in issue for the vertical cylinder spark plug condenser? Guess your new harness will address this if it is. Full harness would have cost you some coin... still in the end, WHEN you do get your bike up and running you'll be happy knowing the wiring harness is spot on.

While I'm here. I read mention of a 'centurion'? is this an add on or a code reader? Actually what electrical add ons do you have? I have a healtech gear indicator which would not play nice if the OEM USB data connector was hooked up.

What about your crank sensor? how old is it? Did the bike start to play up when warmed up (before it finally died)? Is it connected?

Starting to throw a lot of suggestions at you now. Pitfalls of armchair diagnosis I guess...
 

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Fingers crossed. Make sure you post up a result. I'm keen to see you back on the road...

Yeah my crank sensor was throwing up an error code on a regular basis for a couple of weeks. It would simply reset again. As I was having the mentioned issues I gave in and changed it with positive results.
 

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Man oh man, that's every bikers nightmare there. Still, I think you may have dodged a bullet here. You would definitely have notice valve to piston contact mate. Easy to see timing. Find TDC for horizontal, dimple on main pulley shaft should line up with mark on crankcase. Take off the valve cover to ensure its on compression stroke too (ie all valves closed). Don't bother with the dimples on the cam wheels, they're for assembling onto the cam shaft. What you look for is the cut outs on the end of the camshafts. There's 3. At TDC the opposing cutouts should be level with the top plane of the cylinder head and that third cutout pointing away from the cylinder (towards the front of the bike).

So with the Horizontal at TDC, you'll find it should be timed right (as that cylinder was firing). keep turning the engine to find TDC for the vertical (belts should be turning CCW?). It will be the next to fire, so go steady and once vertical is at TDC check the cam cutouts, again the opposing cutouts should be horizontal in the same plane as the deck of the cylinder with the third cutout pointing skywards.

As I guessed early in the thread (post #11), I reckon you're maybe 1 or 2 teeth out on either or both inlet and exhaust which is why your cylinder wasn't firing. This isn't I told you so moment, we should be confident enough in a trained mechanic to do it right. If you did it yourself, well that's a lesson learnt, to properly torque the pulleys, renew the torque nuts and to be certain, perhaps use some low strength thread lock on the tensioner pulley torque nuts.

Next step is to load your shotgun and head down to the fucktard mechanic that caused you all this joy and come to an amicable solution to make things right.
 

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There's a specific tool to hold the cams in position for horizontal TDC and at the same time the vertical cylinder at the correct position for the vertical cams when the horizontal is at TDC. This is needed because when renewing or adjusting the belt tension the cam wheels need to be loosened so they cam move with the belt as it is tightened and secured. Once the belt is down, the cam wheel is retightened to the cam so that timing is retained.

Having renewed my belts, my timing is out by about half a tooth (which is noticeable to me on performance). It runs OK, but its just not quite there on power. When I tightened the belts, I could see the cams move off TDC timing ever so slightly as the belt tension changes.

Still waiting for the tool to arrive. Have sent off an irrate email now, 2 months later with no sign of it having been shipped, grrr.
 

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Fair enough martinc, hopefully you'll get her on back on the road sooner rather than later.

PS... don't mean to state the obvious here either, but I hope that 'the bike can start sometimes' is in the past tense. Don't be starting her up with the belt in that condition ;)

Don't forget to remove the plugs and place transmission into 4th or higher gear to help with turning crank shaft. Its not much more to remove the fuel tank either, makes life a lot easier for work on the vertical cylinder and its just a couple of bolts and a connector.

Checking valve damage, pff, the work log just keeps getting bigger and bigger. If you had an inspection camera, you could through it down the spark plug hole to see if the piston crown has made contact. Otherwise, with the piston at BDC, if you can turn each camshaft with relative ease (belt removed) and no obvious (visible) valve shaft damage??? how far or certain do you want to be? I'm not looking or have heard it run, but from what you've described I think you'd be safe to say there was no contact.
 
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