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Misfire and Running Hot on One Side

Have you tried disconnecting the O2 sensors yet?

Well I'm back to the OEM flash now so the O2s are needed for proper running. I'll swap them left to right when I put the OEM exhaust back on this weekend and see if the temp issue follows the O2 sensor. I'm working the bike back to stock ahead of taking it in as it's been my experience that ANY aftermarket part will ALWAYS be made the scapegoat. "So I see you have an aftermarket license plate frame. That certainly explains your engine oil consumption problem."
 
I had. Snowmobile with exhaust temp sensors on it and one side was always hotter then the other, it never bothered me. Are you hitting the rev limiter? My buddy road my bike and was a experienced rider he didn't realise he was hitting it. He had the same bike as me but I had Todd's 2 into 1 exhaust and maybe the louder sound through him off.
The exhaust temp disparity may indeed be a red herring. Does it cause me problems when I'm riding down the road? Nope. But the misfire sure is. Are the connected? I'm not sure. Maybe. if I can get the misfire fixed and the exhaust temp issue remains, so be it. I can live with that!
 
Did you try and disable traction control? I had a V7II Racer with after market exhaust and ECU reflashed and at 3000 RPM steady throttle just driving it would keep cutting out. I tried all sorts of things and finally tried the traction control off and it ran like a champ. You have to turn it off after each ignition shutdown and start but not a big deal. When running I think you hold the starter button in and press to select through the settings. I don't know why it fixed the issue I only know that it did.
 
Did you try and disable traction control? I had a V7II Racer with after market exhaust and ECU reflashed and at 3000 RPM steady throttle just driving it would keep cutting out. I tried all sorts of things and finally tried the traction control off and it ran like a champ. You have to turn it off after each ignition shutdown and start but not a big deal. When running I think you hold the starter button in and press to select through the settings. I don't know why it fixed the issue I only know that it did.
I have a V71, so, no traction control as far as I know.
 
Made some solid progress this weekend. Put the OEM flash back on the bike but decided to leave the GTM 2:1 exhaust on. Misfire totally and completely went away. Bike felt a little lean so I dropped in my Fat Duc O2 emulators that I used to run prior to the GTM flash. Put about 50 miles on it on Saturday. Ran awesome. Not only is the misfire gone but the left and right exhaust temps are now within 10 to 15 degrees of one another. Flashed back to the GTM flash on Saturday night and the misfire immediately came back. Back to the OEM flash on Sunday and another 40 or so misfire free miles.

To be clear, I dont think there's anything "wrong" with Todd's code per se. He's successfully used it on countless bikes and he's reviewed my file on multiple occasions to make sure it was OK. I think there's something wrong with my bike that only presents itself when paired with the GTM flash. I am still getting P0611 codes, despite the charging system being upgraded to a MOSFET VR and a new battery. So something in there is screwy still. BUT, the bike runs flawlessly with the OEM tune, Fat Ducs, and the GTM 2:1 pipe. Sunny weather is now here in Seattle so I'm inclined to stop screwing with it and just enjoy it. If whatever is causing that P0611 actually breaks something so be it, I'll deal with it then. Until then, I'll ride with a big smile on my face as I listen to that sound of that exhaust.
 
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