You best bet would be to install a 130amp alternator from a 94+ GT.
Here's a link to a tech article about the swap. It's a pretty straight forward swap.
http://www.mustangcentral.net/tech/alternator.html
Also, it should be easy enough for you to build a box that will fit into the hatch of of a Mustang GT. A vert might be more difficult but I'm quite sure it can be done. If you don't feel comfortable building a box, I'm sure a local sterio shop is more than capable of building a box for you.
What size subs are you running? What brand? Number of them?
What's your set up?
L8ter,
Josh, aka the tireburner
P.S. if you have any more questions or want any suggestions, please feel free to post them.