JonatanOTG,
First, I think it's awesome you get to build a guitar AND get school credit for it.   :icon_thumright:
As far as the DiMarzio pickups, I can't recommend the Breed pickups highly enough.  They are NOT just shred pickups; in fact, the neck has some of the prettiest clean sounds I've ever heard, especially with the coil tapped.  I have these in a (non-Warmoth) baritone and the only thing I can't get out of it is the neck+middle or middle+bridge classic quacky Strat sounds.  
As far as pickup wiring, I saw you wanted to move away from the standard 5-way switch.  One of the best mods I can think of for a two-humbucker guitar (with four-wire pickups) is the Jimmy Page-style wiring.  (Yes, I know you're wiring a Strat; bear with me a moment 

 )
http://www.cjs-labs.com/sitebuildercontent/sitebuilderfiles/JPage-LesPaulWiring.pdf
I know you wrote that you "don't want twenty different knobs and switches," but was just sharing various options that are possible.  The coil-tapping is an EXTREMELY useful feature, but I really like the phase option just as much.  Out-of-phase cuts a bit of the low-end (and some of the output) but the high end really cuts through.  And as far as add-on options go, it's pretty cheap to get done.
Anyway, congrats on your project, and hope you end up with something that you quite fancy.
J