I'll buy that for a buck.........

Most bikes run better in cold, dense air.
Especially in 45-50 degree weather, when the fuel is nice and cold as well.
Doing your flapper mod/soft rev mod and removing the air deflectors in the airbox *might* get you a few (1-2) ponies in the top end, and gets rid of that 3500-6K bog. The soft rev mod also gets you another 1K in RPMs and an HP or 2.
Removing the PAIR system helps you lose about 3 lbs, gives you a true A/F reading at the pipes, and stops the constant backfiring out the pipes.