2004 FJR misfiring - any further suggestions?

[raYzerman]

We have an active thread on FJROwners if you want all the gory details over there.. Just a summary here......

I offered to help a local gent here where I didn't feel he was getting good advice.... if you can bear with me for some backstory... he purchased the bike used from dealer (currently has 56k kms or 34k miles on it). Experiencing poor idle and some noises in the clutch. Certified Yamaha Tech did some work, changed the oil (it was black when he bought it, WTF), spark plugs, did TB sync... all on the new owner's dime. He advised that he needed a new clutch basket (but he did not remove anything to inspect, WTF), did not want to do a valve check (too much work, WTF), and advised he would have to take the bike to a tuner to fix the idle (WTF). It seems this tech is lazy, just wants the easy gravy jobs, my opinion having never met the man..... no way this bike needs a clutch basket with that low a mileage.... I'm developing a bad taste for so-called award winning Yamaha techs.

I get the bike, spark plugs are new, slight misfire on one cylinder (I thought), which I determined was bad resistance on a spark plug adapter, cleaned and fixed it. Noticed new caps on the TB ports, so assumed that was done. We verified good connections at the multi-way connectors up by the steering head, bike is actually in good shape.
Oil was relatively clean, removed clutch cover and took the clutch apart. Everything was pristine clean inside, did a clutch soak and put it back together. Very little wear on the clutch basket, looked great. I suspect due to the miss issue, at low speeds there may have been some driveline chucking, checked that, it was normal.
As we let the bike down, we see a nail in the rear tire, so repaired that with a plug. I did not test ride the bike, as we ran out of time, idle miss seemed better. Later it was reported that the miss was not cured.... also it appears to be missing on more than one cylinder intermittently, a bit worse when it is hot, consistently below 4000 rpm, hardly at all above 4000-ish.... I now advised dosing the fuel with injector cleaner for the next few tanks, hoping it would clean up the combustion chambers too in case they were carboned up...... I also advised I would do a valve check to verify no valve is too tight..

Fast forward to now a few weeks later, I have the bike back, test rode it and yep, intermittent/consistent pattern of missing on more than one cylinder. However, it does it a little bit above 4000 rpm, not nearly as much. Has full power if you go WOT, no issues with performance.

Here's what I've done......

Removed spark plugs immediately after test ride. Hard to tell as all cylinders have been firing, but hint of black around the outer rim of spark plugs 1 & 4 (we had a gent with that recently, but bike was running fine).
I removed all spark plug adapters to verify 10k ohms, cleaned them all anyway, snipped a little off each wire and reinstalled (some needed it). Reinstalled plugs in different cylinders.
Started the bike, not cured.
Checked compression, all were dead uniform and healthy. Indicates no carbon on valves, and no valve leakage.
Continued to check / test / verify individual items one step at a time....
Unplug/replug Cylinder Identification Sensor while running (Gen 1 will run, Gen2 & 3 will not if disconnected), tested output voltage is correct.
Check MAP sensor, still clean and functioning. Swapped in a spare I had, same thing, all OK.
Cleaned and refreshed ECU connector, all looked good.
Ran bike with O2 sensor unplugged and re-plugged, made no difference (as expected, would only affect fuel mixture slightly)
Checked no trapped wires at right timing cover, all good.
Went into DiAG, cleared all the codes I just triggered...... 11, 12, 13, 14, 19, 30. Ran bike, no codes have returned.
Checked TPS readings in DiAG, Low 14, High 99. Throttle response is OK, so not suspecting TPS.

Verified CCT has a green dot... good news, but could valve timing be off? Valve check next.....
Valve cover off, dammit, valve timing is OK.... makes sense, bike develops power normally.
Did valve check, found 3 intakes slightly tight below minimum, one exhaust at min.... nothing should be the cause, verified by compression being good.
Reshimmed everything to 70% max.
Removed PAIR system plumbing.
Fire up the bike, problem still exists. TB sync tweaked to perfection.

Swapped in brand new set of Iridiums I had in the stash... better, but condition not changed really.... swapped original plugs back in.

Loosened TPS screws, moved it around while bike running, actually ran better when low end out of spec, i.e, reading 9 in DiAG (should be 14-20-ish). Not cured, but that just told me it was on fresh resistor board... swapped in another (used known OK) TPS, no worse, no better, seemed better when set at 16-18... not that it means much....

Checked each coil, primary and secondary resistances good. Cleaned all the spark plug adapters this time and verified resistance good.
Ordered set of used ebay coils, while I waited, pulled the injectors.
Activated the injectors several times, nothing abnormal, spray patterns looked OK (as well as you can see them), put them back in, can get them cleaned professionally another day.

Installed ebay coils 1&4, condition improved noticeably, not totally cured. Ebay coils 2&3 tested OK but had #3 spark plug adapter resistance way out of whack, and when removed the copper spark plug wire was all green and obviously making poor contact..... I'll bet that's why they were replaced, nobody looked at that.... Installed them and refreshed connections, used a known good spark plug adapter....

Fired the bike up, the misfiring condition was slightly worse..... after installing the injectors, I swapped the original 2&3 coils back in.... fired up the bike, it was better, intermittently misfiring..... but much better than before.

Test ride revealed things were definitely improved, misfiring mostly gone, definitely none above 4k rpm, no detrimental effects on performance whatsoever. Sending bike home with owner to put some miles on it, run a tank or three with RingFree (it has benzine and Xylene, should help injector cleaning). Bike will come back in a couple of weeks, will inspect spark plug burn, etc.

Direction is order another set of 2&3 coils, check that out, will likely replace spark plugs even though these aren't that old... Considered trying another ECU, but I'm banking on the coil issue at this moment....

The saga will continue in a coupla weeks...... one of my points is, do only one thing at a time and verify before moving on to the next step.......

[bungie4]

Man i wish even 10% of mechanics had your skills and diligence.

[FJRoss]

I would have guessed coils/wires after all of that - especially when it seemed worse when hot. I think you have covered that pretty well...
Have you tried misting some water at the top of the engine (in a darkened garage) to see if you have a light show (or stumbling) while running?
Could still be TPS - again typically worse when hot and may be hard to detect using diagnostic function.

The only other thing that occurs to me is the big white connector under the tank - often reported to be problematic in Gen I.
https://www.fjrforum.com/threads/main-e ... ion.22734/

You have certainly put some work into this!

And when it comes to "certified" Yamaha technicians - WTF?

[raYzerman]

I did not mist the engine, but did look for arky sparky in the dark, didn't see any... plug wires are sheathed as well...

Forgot to mention all the connectors under the hood were unplugged, cleaned and verified (they were OK). One of the first things I did.

Yamaha tech's answer was.... "You need to take it to a tuner guy for the idle problem".... WTF.

Between my bad knee and having to take frequent breaks, go to PT appointments..... this has dragged on for two weeks.... Oh by the way, he had a leaky fork seal and contaminated brakes..... blew a half day on that....

[FJRoss]

Got a TPS you can swap in from another bike to check?

[raYzerman]

I adjusted the TPS and I also swapped another one in, which I left in..... if we get back to that eventually, we'll just get a new one.

[Festus]

Man, that sounds way too familiar.

At track day, I walked over to a mechanic that’s a BMW guy and asked him and after a few “did you try this”, answered with “yes”, he said he’d reflash the ECU. Said they do that all the time on BMW’s, the ECU gets some value that gets corrupted and that’s the fix.

I’m beginning to think he was closer than I thought.

[raYzerman]

Today we installed another set of 2&3 coils, all checked out and the spark plug adapters..... didn't fix it, bike has been running much better since our last go, no issues with power or performance, but has a miss throughout the rev range, most noticeable when held around 3000 rpm no load. Swapped in another set of spark plugs, same deal....

Owner is going for knee replacement surgery in a coupla weeks, so we'll not likely revisit this thing until spring..... thinking there's nothing to do but run some RingFree through it, and perhaps a new TPS on the list.

[gitbox]

You've definitely eliminated a LOT!

How about an ECU swap to rule that out? Can you scope the signals driving the injectors and coils at the ECU. Also the signals from the crank and cam sensors. Compare the signals to known good. I can scope mine for a comparison if needed.

[raYzerman]

I don't have a scope, but understand what you're saying...
I've considered replacing the cam sensor, however on Gen1 only, the bike will run with that unplugged, and unplugging it makes no difference... I have no reason to suspect the crank pickup, but yes unknown.
Bike had been ridden normally before it came back to me the other day, spark plugs looked like burning very well...
This whole project is going on the shelf until next spring........

[gitbox]

This whole project is going on the shelf until next spring

Well then... I guess that's that. (I really was hoping for a conclusion - love these deep dive diagnostics)