if those pipes are the hmf dual pipes that sit under the seat ...i had the same problem with the dual devil full system that is under the seat....i did all the above...k&N, power command, zero mapping...and i still had the same problem...when i read sportbike magazine and i read that the more curves in a system the more power u loose...so i took them off and put back on my factory and slip on yosh exhaust...and got back my power...