Well, if this is your first guitar, then i *suggest* that you use something fairly cheap and easy to work with. Alder, Ash, Mahogony, heck, Agathis if you want to; the point is that the sky is the limit. It doesn't have to be traditional to be a great guitar.
As far as pickups go (and i know that people are going to ridicule me for this) I really would suggest Mighty Mite single coils. You could go and pay $50-75 per name brand coil, and get a great sounding guitar. Or, you could go to Mighty Mite and pay $25 per coil, and get a great sounding guitar. I'll put it this way: my brother has a crappy old Squire strat. It was like $120, and sounded terribble. $75 later, his guitar sounded like a $700+ strat. I know they're not brand name, and some people turn their noses up at Mighty Mite, but these pu's are really great. If you do go that route, just make sure you get the Alnico's, and not the Ferrite ceramics. It's probably just personal preference, but I think they sound a lot better, and you'll get a much more fat vintage tone with Alnico.
Thats my $.02.