1st, you should decide exactly what you want. Type of wood for body and neck, neck type, bolt-on, neck-thru, pickup configuration...every last detail. As redawg said,
www.stewmac.com has most everything you need, as well as
www.allparts.com and
www.wdmusic.com for hardware. There are a few eBay stores that sell some interesting neck and body parts--just do some searches.
For pickups, I would recommend a pair of Joe Barden Two-Tones so that you can switch between single coil and humbucker. Unfortunately, Joe has stopped making pickups and these now go for $300 and up on eBay.
There is an alternative pickup that is especially good for metal made by Dimarzio called the MultiBucker. This is a pair of their single coil sized humbuckers in one full-sized humbucker (4 rails). The standard configuration is a Chopper with a Fast Track 1. With a 3 way switch you can select each pickup or both pickups in series. The Chopper and FT 1 are Strat sounding pickups, but when you put them in series, it sounds like a Dimarzio Megadrive and is great for metal. Dimarzio will custom make these pickups per your specification thru any authorized Dimarzio dealer. For a neck pickup, you might want a Fast Track 1 and a Cruiser. If you want a slice of Gibson
and Fender, a ProTrack does a PAF and mixes well with a Strat-style Cruiser. To see what pickups are available, go to
www.dimarzio.com, click "strat" and "hum-canceling strat". Only the rail pickups listed qualify. I don't think you will find the Multi-Bucker on the web site. Its kind of a secret.
...Oh, the freedom of the day that yielded to no rule or time...