Ok, I'm probably not going to be much help to you, as I've never built one from scratch, but oddly enough, I was thinking about it recently, too. I think the most obvious thing would be to go for a body that takes a bolt on neck, otherwise things may get a bit messy for a first build.

Also, you may want to see if you can take a look at the insides of a similar guitar to the one you want to build and take note of the wiring so you have an idea of how you're going to wire yours up.

I guess the last thing i'd say is not to overlook the need for the little things like pick guard/plate screws, pickup bolts/springs/rings etc - do Strat necks come with a top nut? I doubt it..

I'll be interested as to what someone with more experience has to say.
Good luck!

[Edit: Sorry, i didn't read that you'd already got the body]

[Edit #2: Just a thought, but you'll probably need to know how to adjust the setup, too. Things like Intonation, and the Truss rod may (likely will) need to be set. If you don't know about adjusting those already, it's probably a good idea to read up on it.

Ed