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Throttle Position Sensor Issues (Are you Experiencing Poor Idle/Mileage, or Stalls?)

Quick update, found this thread https://www.600cc.org/threads/2011-xj6n-cylinder-1-4-misfire.34266/
TL;DR on hot engine ECU stops driving injectors 1&4, causing misfires and symptoms similar to mine.

I've tried bridging injectors 1 & 4 from 2 & 3, both power and switching contacts, as danny_xj6nUK did.
Confirmed all 4 injectors fire from diag code 37 (screwdriver to ear).
After trying to run bike at idle - this didn't solve my problem: exhaust headers 1 & 4 are still ~2 times colder than 2 & 3.

photo_2026-08-17_15-44-09.jpg

The remaining test on ECU side is ignition. I've already tried swapping coils side to side, which didn't help.
Potential issue could be with ECU driver for cyl 1-4 channel. It's a similar mosfet in ECU that can go bad just like injector one did for danny_xj6nUK. I've gotten a cheap Chinese 2 channel oscilloscope, but haven't figured out how to use it yet. Will look more into it.

 
An update on things done last month:
  1. Dismissed exhaust header temp difference after polishing them both: IR thermometer was lying due to different reflectivity.
  2. Got digital oscilloscope-multimeter combo gadget.
    Scoped coil primaries, look fine. Used this guide as reference wasted spark ignition system testing guide
    1789328235690.jpeg
  3. Scoped injectors, look fine as well.
  4. Measured CSPS again (on spec) and inspected reluctor teeth for dirt and damage (none).
  5. Played around with C0/C1 settings: moving either direction from default 5/6 makes bike run even worse.
  6. Cleaned, polished, tightened, electro-lubed ignition coil primary contacts/harness terminals.
  7. Measured coils, re-cut HT-leads and tightened connections to cap boots, again.
    Both Coils measured resistance on spec: caps ~10K ohm, Primary ~1.8 ohm, Secondary ~36K ohm.
    COILS_SEPT.jpg
  8. Did an extended spark plug spark test: moved all caps at least 10mm away from engine ground and inspected the spark.
    It turned yellow due to distance but all 4 still jumped properly with diag test.
  9. Installed new manual CCT, it nicely removed most slack out of cam chain, confirmed by rotating engine with a wrench clockwise and adjusting CCT bolt. Left couple mm of slack, closed up cover and ran a test for 5 minutes. Opened up again and confirmed chain doesn't chew up followers.
  10. Removed frame sliders, slackened all engine mounts, dropped engine onto jack and centered all mounting holes. Replaced upper mount bolts with nicer titanium flange ones that are closer to OEM ones.
None of that made any dent in bad vibrations 5-9K rpm. Bike is still insufferable to ride.

Current plans:
  1. Ordered a bunch of DYI stuff around Arduino for measuring vibrations. Will slap them everywhere across the bike and collect more tangible data on vibrations.
    Slop tells me characteristics of vibration can tell what and where is wrong with the bike e.g. if it's a harmonic of stiff element or some rotational imbalance somewhere that depends on RPM.
    Ordered cheap piezo contact mic for guitars as well, for same purpose.
  2. Do a hot coils test: heat them up real good with hair dryer and measure resistance, put them hot into bike and do another spark plug/distance test. They're still suspicious to me. This dude was hunting down misfire source on his FZ6 for several years, touched coils along the way to doing other stuff on the bike - and this magically fixed the problem.
    It's hilarious that he went on to own two other Yamaha bikes after FZ6, and both also had similar misfire problem.
  3. Scope coils secondary (HT leads). Need induction probes for oscilloscope, on their way.
  4. Try finding local FZ6R-F/FZ6R-N owners.
    I saw at least 5 of these bikes around with local plates.
    Maybe I can ask for a quick ECU/coils swap test for a reward.
  5. Measure more air sensors: Air pressure sensor on the throttle bodies, Air valve solenoid on the hose going to valve cover, Air temperature sensor going into airbox. Low priority and no error codes unless I remove any of them and turn bike on.
  6. Cylinder leakdown test. I don't have a compressor, not keen on getting one just for this and all 4 cylinders measured good compression (200 200 200 195 psi), so I don't expect anything wrong here, but still should do it if there is an opportunity.
  7. Previously tried bridging injectors 1&4 from 2&3 power & switching wires. Need to try the opposite: bridge 2&3 from 1&4.
  8. Tried rotating the TPS to get over 90 max throttle value but it's impossible to undo upper bolt without prying right end of throttle bodies up, or removing them entirely. TBD
  9. Not confident in new Chinese Jesben injectors. Need to do priming pressure hold (leak) test.
    Also ordered simple cleaning kit for old original ones since I was not able to find ultrasound cleaning service locally. Still a mystery why bike failed CO emission test this year and had to have C0/C1 dropped to -70 to pass it.
  10. Cam chain & sprockets replacement.
    Found more or less affordable offer, its a big job but I'm more or less confident I can do it in 1-2 days.
    Reference:
    After new CCT removed most slack on chain without any effect on vibration - not inclined to blame cam chain for vibes anymore.
 
Have you considered dropping a small camera down each of the spark plug holes and veiw the tops of each piston?
The idea I'm presenting is excess carbon on the domes of each piston:this can cause vibration,etc. in multi cylinder engines if there is an uneven amount on certain piston domes,compared to less on other pistons.
 
An update as various stuff for the bike starts to arrive.

I bought a guitar piezo contact mic to try and measure frame vibrations.
It measures frequency well but not amplitude, but I've got my own body for that which says "TOO MUCH!".
1790101285996.png

The vibration corresponds to 2×engine RPM and scales linearly with RPM.
Slop tells me this is inherent inline4 engine vibration and lack of 1-1.5 order peaks means all cylinders are contributing evenly. If one pair was underperforming (ignition or fueling) - it would show up on the data.
So now either one component is rattling, increasing amplitude of natural engine vibrations, or all cylinders run equally badly so bike vibrates more than it should.
1790101168683.png

Current plans:
  • Now I will run around the bike like a doctor with a stethoscope and record vibes from various parts.
  • Don't trust Chinese replacements so I'll clean original injectors with new kit I got and put them back in together with old O2 sensor.
  • The cam chain is shipping and I'll replace it, adjusting valve lash myself while I am at it.
  • While throttle bodies are off - I'll adjust TPS so it's max value is closer to 100.
  • Will look around cylinder heads when I take valve cover off.

Two suspicious points during recent test runs:
  1. I had a really hard time holding throttle steady around 4K RPM. Would suspect faulty range in TPS but it transitions from min to max smoothly in diag menu. IDK what to make of it. Maybe I will replace it too, found a ~90 euro one locally.
  2. After 6K RPM I can clearly hear engine "clapping" or loud bubbling sound, that doesn't sound normal.
 
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