Help please. PCIII problems.

[Tito]

I fitted my new yoshi TRS slip ons, and a BMC filter a few weeks ago. I also fitted a Power Commander III. I am planning to get it dyno tuned when funds allow, but in the mean time have tried various downloaded maps, including the one for yoshi slip ons and with/without after market filter, but the bike does not run well at all, particularly around 4,000 rpm. The best I can get it to run is on the map for an after market filter only, and it's still not great.

Anyone got any ideas? It would be greatly appreciated.