Aussie there could be a million things going on here..but I bet it's something simple.

First off..is that a custom map on your PCIII or a standard one. Each bike is different and a basic map will get you by..but a custom map will make both you and the bike much happier.
Also when you changed out to the hypercharger did you plug all the EPA stuff? If not this can cause some backfiring and popping..but usually only on decel.
Also check the pipes at the heads and make sure they're not getting a leak. This will play havoc with the bike. (I just get in the garage and use a candle or something next to the heads and see if it gets flickered by an exhaust leak)
