Hi snowcolt. I never cover my 360's with anything, although I think we talked before about this, I have a veriable rage heat gun, so i can control how much heat to the board. and I just stay away from the caps. I have used aluminum foil at a time or two, to keep heat off of someparts.
So I would wrap up the capacitors with aluminum foil and then cover them again in aluimnum foil that should keep enough heat out and keep it from damaging anything to be on the safe side. also I remember you said you heat guns around 750 degrees, I wouldnt put it as close, maybe stay back 2 or 3 inchess so you dont desolder nothing off the board.
I also use one of these for checking the heat of the griddle and the motherboard on the cpu and gpu to keep a eye on the temps can get them at home depot
http://www.homedepot.com/h_d1/N-5yc1v/R-100674438/h_d2/ProductDisplay?langId=-1&storeId=10051&catalogId=10053