I've never before had a Mega getting hot, I'm running one on X8 and one on quad.
Carbonquad is flying Pro Mini, on that one the regulators on the MWC board get very hot when powered by anything else than BEC.
I'm flying 3S and 4S depending on situation (which ever are charged)
Do you have a buzzer? You need to move that the furthest away
MAG prefers to have a 3 to 5 cm clearing around it too, supposedly. But that's never going to work on IMU's :P