Don't mean to beat a dead horse, I know this has been talked about a good amount, but I've searched for some posts previous and nothing quite sounds exactly like mine.
06 SB with PCIII and stage 1 intake starts up and runs great for about 1 minute. after that, when at a cruising (steady) throttle it will skip and run on 1 cylinder. If you ease into the throttle it will only get worse, but if you snap into it it comes right out of it and runs like it should. Either full throttle or no throttle is the way it likes to run.
When you let off the throttle while in gear it will pop, shoot flames, all that bad stuff. Removed PCIII, no change. Changed plugs, no change. Checked connections for corrosion on ECM and coil, none present. Does anyone know what the resistance for the coil is supposed to be, because I'm narrowing it down to coil or injectors.
Funny thing is once the check engine light comes on , it runs perfect. I dont know if it is retarding the timing or what. Sorry for the long post just want to put all the details into it! Hope someone has had this problem before or can help me out.

 

Not sure about this but it almost sounds like the bike is going into parade mode where it shuts down the rear cylinder to prevent overheating. Not that familiar with that feature but I have seen discussions about it here on the forum. Might be worth a try.....Good luck and let us know what you find...