Thinking of running a similar system on my 96 c2500. I think with your drop and the gas tank layout your going to have a problem getting equal length pipes coming off the exhaust manifolds to your y-pipe. The best position I can think of off the top of my head without going into the parking lot of my work and crawling under my truck would be on the passenger side of the cab, but either way something is going to have to snake over the transmission at a spot that's compromising for a lowered vehicle (mines static 3/4 so not as bad) Just my .02 and I would love to hear a better option from someone else, as I'm in the same boat.
I would skip the x-pipe, as you're going to be joining them in a single exhaust anyways. If you want to reduce noise try using a large case muffler or possibly a cheap glasspack (as a resonator) along with your muffler of choice.
325hp at the flywheel sounds about right to me.