UR B-hind Da 8 Ball
Join Date: Jun 2004
Location: East TN
Bike: '03 R6, XR400, V-Star
Re: 03 r6 rough idle
Sounds like coils to me. I did have a problem with a PowerCommander III, the bike would shut off sometimes when decelerating into a turn around 10K rpm. But DynoJet replaced the unit and I've had no problems since. From your description, it sounds like you have a PC V, correct? If so, that is probably not your issue, unless you have a bad connection in the PC wiring harness.
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I find a Soap Box comes in handy to get on my High Horse!