TDPRI has just such a thread
here.
That said, you have some decisions to make for the body.
Bolt or set neck?
If bolt neck, Tele or Strat route?
What kind of bridge?
Tele(single, humbucker, P90) top-loader or string-thru, TOM with stopbar, TOM with string-thru, Strat hardtail, wraparound or tremolo?
If tremolo, FR, Bigsby, Strat 6-screw or Strat 2-pole?
Some bridge styles will require either an angled neck pocket or a recessed bridge.
What scale?
This will determine the location of your bridge.
Number of pickups.
Multiple pickups and type will help determine location as will the number of frets/length of fretboard.
Controls?
Control route on the top or on the back?
Strat or Tele style top route?
Output jack on the top or on the side?
Number of controls. This will be determined by the number of pickups.
I'd recommend something simple to begin with.
Those are the necessary basics.
The body shape is an esthetic/comfort thing.
The only other important decision is wood selection and whether it's going to have a top or not.
Warmoth has good info on
wood selection as does
this article by Frank Falbo.
The
Warmoth guitar body builder is a good place to start playing around.
To make things simple, I'd suggest a bolt neck using a Mighty Mite neck.
This would make it a 25.5" scale build.
You can get these on eBay for under $100 new at any time.
I've got a book that demonstrates a simple starter build like this and includes full plans that can be used to make a copy of that guitar.
It's called
Build Your Own Electric Guitar.
Pretty straight forward. lol