Normally I would say to bypass the PowerCommander, and run only on the factory ECU. BUT, you mentioned a big bore exhaust? I'm assuming you mean a full aftermarket header system, like a Akrapovic or Jardine 2 into 1?
For sure your bike will run lean without the powercommander, so not sure this is the best idea, I'm just trying to eliminate the easiest possibility first.
Try it for just a little bit of a test to see if you still have your symptoms.
Hopefully SubSailor, Miller, LDH, or Madbuyer will be along shortly. They know way more than me about electrical.
edit: I see this is your first post. Welcome to the forum, hope we can help you get the problem solved.