The problem I foresee with the mag idea is maintaining the right pressure. Too much pressure on the spring will crush your paint, not enough and it won't feed. It'll be especially difficult as you'll need enough pressure to hold a single paintball in the breech and ready to fire. Too much pressure and you'll just be forcing paint down the barrel. There is also the issue of keeping the clips in the marker - I don't know how easy a catch/release mechanism will be.
I've considered building an underslung hopper for my US-5, and my idea was to build something that looked like a c-mag. That way I have something that I can still bulk refill (it would be permanently attached, to avoid the complications of a clip release mechanism and altering the feed), but it still looks realistic. I'd be similar to some of the SAW box magazines that people have done, with a slightly different look.
As for the airline relocation, first thing you might want to try is macroline, it will be much more flexible than the steel braided hose. It will be vulnerable to liquid CO2, but as long as you anti-siphon your tank you should be okay. I don't think there is any way around fashioning a custom mount for the tank though.
For the stock, I'd start with a simple butt cap for the tank. It won't look as real, but it's simple, cheap, and gets the job done. It'll also be easy to remove - something that is very crucial for refilling your tank!
Not trying to be discouraging here, but I'd hate to see you cut into your marker only to find that something didn't work! I've thought the same thing (I'd love my US-5 to have a good MP-5 look, without all those hoses and hoppers) but the logistics of the conversions are pretty rough.
2003 ICD BKO w/ 45/4.5k, Ricochet Apache
'98 r/f Autococker w/ 45/4.5k, J&J Edge kit (14"), Ricochet 2KX
PCS US-5 Mech. w/ 48/3k, J&J Edge kit (10"), cyclone feed, JCS folding voodoo stock with RVA
Kingman Hammer w/ 13/3k, J&J Edge kit (14")
Projects in the Works:
'99 r/f Autococker w/ 45/4.5k, J&J Edge kit (14"), and THE CYCLONE!!!