Good question. I get most of my parts by sifting through yahoo auctions here in Japan. I have a few other sources bookmarked on my home computer but I can't recall them right now. We definitely have to do a bit of digging..
I bought two bridges, pickguards, bodies, and necks from Warmoth and was pleased. I do most of my own wiring but I generally get my smaller electronic parts from guitarpartsresource.com.
For left handed staggered strat pickups, I have Dimarzio's. There is a company in Harrisburg PA that has some or can get them. I think the link is www.mikes-music-shop.com