I'm finally going to build a partscaster. I've played with my cheaper guitars and seen many youtube videos, and I'm pretty sure I know exactly what to do as far as installation.

How are the mighty might necks/bodies? Since they are licensed by Fender, will Fender hardware drop in with no issue? Also, is a used neck worth the risk? A used body obviously is, but I don't want to deal with a warped neck.
You mean MightyMite. yup they sell parts, and pickups. I assembled a few Fender Partscasters with Fender MiM body and neck, then got USA parts with upgraded pickups and electronics.. The guitar cost more than a new Fender MiM strat... not exactly economical.. if you plan on making a fun guitar, just buy a quality donor guitar (complete) and upgrade the components, way cheaper than buying parts for a build.

Rondo has some nice guitars than don't cost an arm and a leg, I am eyeing this SX Furrian but I already have too many guitars to justify buying another.
http://www.rondomusic.com/furrianrnssspbu.html - tele style modern player... cool color too.
I have Washburn guitars 'Maverick Series' and bass 'Bantam Series' and a few pedals and amps, but man I wish to have more patience and drive practicing my playing, if it's equal to the modding itch, then I'm golden.
^^What he said. Unless you are going for some exotic woods or bizarre pickup configuration in a rear routed guitar, then going custom from the ground up is just spending more money than you have to. MM only uses common woods--swamp ash, a little alder--so you are are better off taking the above advice.

But to answer your question. Having used MM bodies, I have never had any problem with genuine--or parts made to genuine spec--Fender parts fitting.

As far as your neck concerns go I have bought a lot of used guitars over the years and have never had a neck issue that wasn't correctable with truss rod adjustment and the usual setup. If a neck is jacked up then it is usually pretty obvious by looking at it.