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So, I recently purchased an ‘08 R6 with 2500 miles that had been sitting for a while and did a full tuneup on it and it was running fine. This past week I put on a full exhaust, new spark plugs, and sent the ECU out to get flashed and I started noticing some issues. I noticed today that when cruising above 9000-10000 rpm’s, I’m getting engine surging, losing power then regaining it, even though I’m holding the throttle steady, which doesn’t happen at lower rpm’s (8k and under). I’m thinking it’s either the secondary injectors, the map on the flash, or there’s an exhaust leak but I could use some other opinions. Any help appreciated. Thanks.
 

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YZFR6... ooodles of HP
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As to secondary injectors, they only activate when you really roll on throttle. At a constant throttle, the mains do the heavy lifting. I'd look at the plugs and coils. Sounds like spsrk energy isn't up to snuff.
 

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Stock ECU programming accounts for AIS and EXUP systems in the oxygen sensor feedback. Could be leaning out. Had similar cruise issues with a prior car but was caused by excessive back-pressure from the exhaust system. Disabling EGR operation via unplugging a related sensor served as a temporary workaround until the catalytic converter was gutted. (It BTW was only clogged as a result of the the engine running too cold over a period of years.)

Bottom line, your programming is likely invalid as a result of the exhaust changes.
 
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