I have a full Akro System. BMC filter and PCIII with presumably the proper map. I get lots of popping on closed throttle decel and an occasional flame. My question is how bad is this for the engine. Am I burning out an exhaust valve or something, or am I just annoying the neighbors?

presumably you still have the SAS system plumbed in.....if that is the case and you haven't taken if off (using the SAS delete plates on the side of the engine) or switched it off in Tune ECU.... then Yes its totally normal and if your not seeing flames out the back then try harder!!!!!!!!.... my wifes record is about three feet of flame with me following her!

Could be the graphite seal in the exhaust. They don't last long and will cause bangs and pops. Do a search for graphite seal. They don't cost much around £8.

I'd start with a double check that you're running the correct map. The OP of my bike was told the evo akras was a "slip on" and there was no need for a re-tune. The bike baclfired and popped on decel incessantly.

Switching to the Akra Akra map has made things 95% better. I only get the occasional pop when it's below 50 degrees or so.