If it's possible to control timing with the PCIII definitely reduce the timing advance in the problem areas.
I have a PCIII that I haven't installed because of a lack of good maps - I've heard a few times that the ones from the site are junk.
Lots of places do dyno-tuning for Power Commanders - finding someplace local and having a map made for your bike would lead to the best running, but it ain't cheap (whereas I am

).
GL with it and let us know if you find a fix.
