Its great fun building a parts-caster, and since you can choose all the options to suit you I see less and less point in buying an "off the peg" Fender.
Good luck with your project!
There are many options out there. I would start by thinking of the sound you want. For a "typical Fender" tone, you won't go wrong with an alder body. Then choose trem or hardtail bridge, and what type of pickups you want (humbucker/single coil) - these will affect the body routing.
For the neck fingerboard, maple for snap, and rosewood for a bit more warmth. Do you want a big 70s headstock?
And then stuff sort of comes together ;) We'll help you if you need it.
An unfinished body will be cheaper - as long as its decently sanded, you can attempt a dye+oil finish yourself.
MrBump is right on the setup, its worth doing that, especially if you have a completely new neck needing a fret dress.