999 troubleshooting nightmare! (any help would be appreciated)

[psycledelic]

I am about at my limit of sanity with the 999s that I bought a couple of months back.  Here is the scoop:
Bought a used 04 999s from an individual two months ago.  He was the 2nd owner.  Bike was originally purchased at the shop that I bought and have my Monster serviced.  The 999 has had all of its services at the same shop as my Monster.  It had 8300 miles on it when I bought it.  No issues as time of purchase.  

I started noticing a studder after about a week (mostly when I first started it up).  That turned into it missing and backfiring.  I had already set up a used bike inspection appointment at the shop, but the Duc techs were at a training seminar for a week, so there was a wait before I could get it in.

 When they did the inspection, the diagnosis was that the vertical cylinder wasn't firing every time.  Not sure what, or how they check, but it was determined that the 54mm Termi ECU was OK and that the problem was mechanical.  So, new plugs, plug wires, belts (belt had a small nick) were installed.  Valves were all OK and were within tolerances.  No issues with the piston or other enternals.  They switched the coils, plugs, wires, etc. to the horizontal cylinder and everything worked (but, the same parts that were originally on the horizontal cylinder failed on the vertical). So, they focused on the ECU again (apperantly, the ECUs on that year model has some issues).

 The service manager at the shop located the original owner, who still had the stock ECU / exhaust, and asked him if we could use ECU to test the bike.  He was nice enough to bring it up to the shop for a test.  No luck, the vert cyclinder still failed to fire.  So......, if the bike is OK mechanically, and the ECU seems to be OK, what the hell is wrong with it?  Or, a better question would be, what else needs to be checked?  

It is obvious that the tech working on it is very frustrated with it.  As am I.  I have no issues with the service department, they are being very cool about the labor/hour charges.  Nor do I have any issues with the tech.  He is keeping very detailed records of what he is doing and is keeping all of the parts (belts, plugs, etc.) that he replaces to show me why he did so.  I just want the make the beast with two backsing bike to work.  Now, I am no mechanic, so my explaination might be confusing, but if anyone has any suggestions, ideas, anything that might be a help in diagnosing the problem(s), I would greatly appreciate it.  

In any more detail is needed, I can find out and get the info posted.  So, anything you got, boys and girls!

[J5]

could you use some paragraphs as damn hard to read it

from what i can gleam

new parts were installed on bike

you have a problem with the horizonal cylinder not firing

parts were then swapped from the horizonal to the vertical cylinder

the problem has now moved to the vertical cylinder

is that right ?

if that is the case and the problem moves then it is a problem of 1 of the parts not the ecu

swapping parts 1 by 1 should show you the faulty part

[DarkStaR]

could you use some paragraphs as damn hard to read it
...

parts were then swapped from the horizonal to the vertical cylinder

the problem has now moved to the vertical cylinder
...

+1 on the paragraphs

Parts were swapped, but the problem stayed.

...

So is there, or is there not a spark at the cylinder in question?

Did they check fueling to the cylinder in question?

[Raux]

wiring harness for the vertical cylinder?

[Howie]

Were they able to tell if the problem is spark or fuel?  They could try swapping injectors.

[ducpainter]

999/749 as well as 848/1098 have had some harness issues.

[Speeddog]

999/749 as well as 848/1098 have had some harness issues.

+1, sounds like a harness issue to me.

Problem stayed on the vertical cylinder when suspect parts were swapped, and when the OEM ECU was installed.

[psycledelic]

could you use some paragraphs as damn hard to read it

somewhat corrected.  Sorry!

Were they able to tell if the problem is spark or fuel?  They could try swapping injectors.

Spark.  When the cylinder does fire, the bike backfires like a Howitzer.  I assume that is from the built up fuel. 

+1, sounds like a harness issue to me.

Problem stayed on the vertical cylinder when suspect parts were swapped, and when the OEM ECU was installed.

I called the shop and asked about the harness.  The service manager said that the tech checked the wiring with a cyloscope(?) and it was OK.  Sound right?

[Howie]

You mean oscilloscope?  That instrument takes a picture of what is happening when your cylinder is firing in voltage and time.  Great tool, but it does not check the wiring itself.  It could offer great clues though.  I would try speaking directly to the tech. 

[Bill in OKC]

They could try swapping injectors.

It sounds like that is just about the only thing left.  I've heard of injectors getting stuck open and flooding the cylinder.

[psycledelic]

You mean oscilloscope?  That instrument takes a picture of what is happening when your cylinder is firing in voltage and time.  Great tool, but it does not check the wiring itself.  It could offer great clues though.  I would try speaking directly to the tech. 

Yeah, oscilloscope is what I meant.  Just didn't know what it was or what it does.  I agree about talking directly to the tech.  There always seems to be info lost in translation when the service manager is the middle man during a phone conversation.  I am going up there again tomorrow.  Is there any documentation on an issue with the problems with wiring harnesses on or around that year model?  It would be nice to have something to show him.  I would prefer to not come off as the clueless, dickhead customer in the service bay that is trying to tell him how to do his job.  They are being VERY cool about the labor charges on all of the troubleshooting time that has accrued.  I don't want that to end.  

[Speeddog]

Unless I'm missing something, all the primary suspects have been scrutinized and checked individually, and all suspects are deemed healthy.
Yet the bike runs like crap.
Clearly one of the suspects is your perpetrator.

I had my OEM S4 ECU go bad, lost the vertical coil output or signal.
I swapped all things swappable, coils (coil on plug, so no wires) and injectors.
Engine runs crappy when the injector drivers are crossed V-H.
Due to the immobilizer, had to borrow a complete S4 setup to confirm that my ECU was fried.

I've had bad grounds make a bike crank crappy and not start.
Voltage that the ECU was seeing during startup went too low, spark output got flaky.
Engine wouldn't light.

AFAIK you can swap the injectors.

My money's still on your harness malfunction.
I include all the connectors as a part of the harness, the connectors are the usual first suspect.

[psycledelic]

It sounds like that is just about the only thing left.  I've heard of injectors getting stuck open and flooding the cylinder.

The tech said that he had ruled out the injectors being the problem.  If they were flooding the cylinder, would that cause the cylinder not to fire?  

[psycledelic]

Unless I'm missing something, all the primary suspects have been scrutinized and checked individually, and all suspects are deemed healthy.
Yet the bike runs like crap.
Clearly one of the suspects is your perpetrator.

I had my OEM S4 ECU go bad, lost the vertical coil output or signal.
I swapped all things swappable, coils (coil on plug, so no wires) and injectors.
Engine runs crappy when the injector drivers are crossed V-H.
Due to the immobilizer, had to borrow a complete S4 setup to confirm that my ECU was fried.

I've had bad grounds make a bike crank crappy and not start.
Voltage that the ECU was seeing during startup went too low, spark output got flaky.
Engine wouldn't light.

AFAIK you can swap the injectors.

My money's still on your harness malfunction.
I include all the connectors as a part of the harness, the connectors are the usual first suspect.

I agree that the wiring harness is quite possibly the problem.  Is there a certain procedure to check that, or am I gonna have to by a new harness and hope for the best?

[Speeddog]

Electricals are a kick in the ass, aren't they? 

You can check a bunch of pins on the connector.
There's quite a few.