O.K. - First of all, the most important thing to ask is WHY are you doing this? If you are doing it because you think it will be a fun and educational experience, then go for it. If you are doing it because you can't find what you want out there, great! Go ahead. If, however, you are doing it because you think you are going to save money doing it, stop. Don't do it. You absolutly WILL NOT save any money by doing it yourself. I can save money doing it myself, but only because I already have a shop built up expressly for the purpose of building guitars. You, I'm guessing, don't have that. But, it is a fun process, and you will learn a lot. If that is what you are after, building a guitar will be one of the great joys in your life. Really, it's a lot of fun (why the hell do you think I keep doing it - it sure ain't for the finacial rewards)!
As far as the sounds of different woods, both
Warmoth and
USA Custom Guitars have pages which do a good job of describing the tone of various woods, but you have to remember that the pickups will have at least as much effect (and probably more) on the frequency spectrum of the guitar. The place I think you get the most effect from the woods is in the shape of the note (what keyboard players would call the ADSR - Attack, Decay, Sustain, and Release).
So, go forth, have fun, and build a guitar you can be proud to play.
Light
"Cowards can never be moral."
M.K. Gandhi