I have a friend who built one and he put his on the inside of the pipe. Had it for almost one year and does a lot of riding and no problems overheating. I'm about to build one for my wife's ATV and going to do it just like his. He did mount it almost vertical on the side in case water did get in the tube, the amp wouldn't get as wet. He has tie wraps holding it on the side inside the tube.
I'm also looking at building one of these. The overheating question is one I've been pondering also. The other one is how do I hook the amp up to my mp3 player. The other is how small can these be before they build up too much heat. I've also been thinking about building a system into a moulded rear rack box.
If you have any pics of assembly and how everything goes together would be awesome.