I take it you loaded a canned map and let the autotune module handle the VEs? Do you have any idea what the PC did to the target Lambda and spark tables? Also, the PCV adjusts timing the same way it adjusts target AFR/Lambda and VE; through offsets. I take it you didn't change them from the canned tables?
It's my belief that by altering the main Lambda table and correcting the VEs, the motor would take a fair amount more timing. If I'm right, you could see a substantial improvement in smoothness, power, and economy.
2014 KLR650 NE