Do more Autotune runs. Run autotune, export the tune, then load that tune and enable AT again, repeat a few times. Changes will become more subtle after a few passes.
Intentionally make the bike pop and gurgle as much as possible. You need more hits in the cell that needs attention before the changes will be applied. You can configure the hit count to a lower number, I think default is 50 hits before PV includes it. Remember when you are autotuning you are running .981/14.6 air fuel for everything below 80KPa. So some popping is likely on upshift and decel with really free flowing pipes.
What pipes and mufflers do you have? What cam? (although it looks stock or low end biased cam from your VE's)
<edit> OOPS... my reading comprehension strikes again... FM head pipe, open supertrapp...
Last edited by rageglide; 07-22-2013 at 12:04 PM.