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So, I'll keep this brief even though it's been a 6 month process. My 2007 R6 is currently having the following problems, which started after I had new ignition coils and spark plugs put in.

1. Randomly (no correlation between gear, speed, or rpms), the bike will bog down, sound like a V-twin, and the check engine light will come on. It will stay alive with throttle, but when its closed code 34 (open or short detected on cylinder #2 ignition coil) will pop up on the dash and the bike will die. The two times this has happened I have pulled over, let the bike sit for a minute and when I start it up the code clears and runs fine again.

2. Sometimes at high speeds (120mph +) if the throttle is quickly closed, the check engine light will turn on for a moment and then turn back off. Bike doesn't die and rides fine afterwards. After stopping, any combination of error codes (33 - 36) will have been thrown. This problem hasn't happened since I had a valve adjustment done last week, but there's only been a 500 mile difference between the start of these issues and now. It never had these problems before then.

3. At TOP speed the check engine light will turn on, error code 34 will pop up on the dash and the bike will completely die (regardless of throttle opened or closed). Additionally, looking in the diagnostic menu reveals that all cylinder codes (33,34,35,36) have been thrown. Bike will start back up, but continues to sound like a V-Twin and the codes won't clear. After bringing it back to the dealership that put in the coils and plugs they said that the ECU was fried. At this point I believe that I have fried the new (used) ECU that I placed in the bike after frying the original. This is unfortunately the only issue that I have been able recreate on demand. Sadly, none of the shops in town have a dyno or similar machine that I can get the bike operating at that speed on with sensors hooked up to it.

Up until any of these three issue occur the bike runs absolutely fine, no performance issues whatsoever.

The performance and electrical mods currently running on my bike include: HID headlight conversion kit, Speedo Healer, GTYR Slip on, and a BMC Air filter. I took out my PVC and the bike continues to have the same issues.

Here is the list of parts and things that I and a number of shops have done in attempt to solve this issue (leading up to an occurrence of problem #3 last night):
* New Rectifier Regulator
* New (Used) ECU - Probably fried as of last night
* New Fuel Pump (found out my original was pumping 10lbs off of spec)
* New Stator
* New Battery
* New (Used) Sub-wiring harness from main harness to Coils
* New (Used) Main wiring harness (including relays)
* Valve Adjustment (Bike has just under 27,000 miles on it)
* Throttle Body Sync
* Crankshaft Position sensor (Pick Up Assembly) tested and confirmed within spec, but not replaced.

At this point I believe that despite the coils being within spec (confirmed by two shops) that there is something wrong with them when they're hot. I'm thinking that my next move (in addition to probably purchasing another used ECU) is putting new plugs and coils in again.

If anyone has any ideas or suggestions I would greatly appreciate it. I've been fighting this issue for 6 months now and it's driving me crazy.
 

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I highly doubt you have all 4 coils go bad at the same time. logic just says its highly unlikely. it has to be the wiring. and quit buying used junk. you don't know what you're getting. you could be chasing your tail with bad parts replaced by bad parts.
do not buy used coils. bite the bullet and buy new. www.partshark.com you can always just buy one for now and see if one of the codes goes away.
 
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