I think you may have just fallen victim of some bad luck, McIntosh makes incredible ****, I don't think it would just blow up like that, regardless of whether it was upside or not. I would only have your buddy work on it if he really knows his **** and make sure he opens it without damaging any of the labels that say "warranty void if seal broken". Best bet is to let McIntosh fix it and they may just replace it for you if you happened to get a bad one. I recently changed up my installation and elected to take out my spare tire and install my apps there. It keeps them out of sight and allows me the full usage of my trunk space (except for the big ass dual 12"s!! I wanted to put them upside down on the trunk lid but the heat thing, from the amps plus the fact that my car is black deterred me from doing that.
