I know the kind of sound I want and I know how I'm going to build the thing but the tonal theory is what I'm lacking. :?
All you need to do is pick up a Theory I book for that one; i'd recommend "Elements of Music" by Joseph Straus

:roll:
But more seriously. If you are looking for Dino's tone you are gonna most likely want Basswood as he exclusively uses Ibanez guitars, and i don't think he is into the S series either. I don't really know or care much about him these days, so that is really the extent of my knowledge in that area. As for the others you mentioned i don't really have a clue. The guy from Lamb of God most likely uses a Mahogany guitar as i think those guys use ESPs, but again i could care less about them so i am not the best person to ask about the individuals you mentioned. If you are really adamant about using the exact woods these players do i would recommend trolling around the internet, the band's websites, their guitar companies' websites etc. to find the necessary info.
I can give you advice on body woods for their tonal properties however. If you want rich warm tone with bite go straight for the Mahogany my friend. However, those individuals unworthy of Mahogany claim that it is too heavy. If this is the case for you, and you are entirely unworthy of such a godly wood, then go straight for the Swamp Ash. You will not get as rich and warm a tone as you would with the Mahogany, however, it comes as close as it gets and is quite a bit lighter. Koa is a nice warm tone wood, although VERY expensive. Korina is also quite balanced, and if you get Black Korina it looks damn cool! Don't know much about Paduk, but it is also supposed to be a really nice tone wood!
Necks i would also recommend a bolt on. I tend to think that the neck-thru is somewhat of a masterworker's craft and if you fvck it up, then you essentially wasted your money on perfectly good woods. You could either do a 1 piece maple or 1 piece mahogany, i would stay away from multiple piece necks on your first build as they necessitate meticulous exactitude. With a 1 piece at least you can work down on one piece instead of having to build up to one piece and then working down on it. Others more knowledgeable, correct me if i am wrong, but if you use maple you are sure to get a bit of a brighter tone than if you used mahogany for the neck just due to the actual wood density and close knit grain of the former.
Fretboards you have several options: Rosewood, Ebony, Maple, and some more exotics like Macassar Ebony (very similar in nature to "regular" ebony), Zircote, Purpleheart, Cocobolo (relative of rosewood), and quite a few others. I would stay with the first three for your first build however because when purchasing outside of that trinity things get rather expensive and, depending, harder to work with. Ebony is a bonafide PAIN IN THE ASS to work with. However, in the end it is worth it for fretboards because you could do just about anything to it, save shoot it with a projectile, and it will hold up pretty well; I.E. - great long life, low maintenance, superb feel. I cannot speak for maple as i don't own, nor have made, any guitars with maple. But rosewood is still pretty good, pretty low maintenance, but is A LOT easier to work with.
Tonal qualities of "the beginner's trinity":
Ebony: TIGHT grain, which means bright. However, if used in combonation with a nice balanced wood such as Mahogany or Swamp Ash the results should be pretty good, if not extremely pleasing in sonic properties.
Maple (Flame, Birdseye, Rock): TIGHT grain, again this means bright. Same aspects of combinations apply. You should be very conscious of the combinations you choose as they will greatly effect the tonal properties of the guitar.
Rosewood (and its relatives): Should be nice an warm but hard enough to stand up to a beating, though not like ebony can

. If prepared right it will feel very pleasing to the touch and a pleasure to play. I have a rosewood fingerboard on one of my guitars and it plays like butter!
Purpleheart: Surprisingly balanced and yet VERY durable, good choice for an "out-there" exotic look.
I can't really speak for the other woods because i am not that experienced of a builder yet. I can say, however, stay the fvck away from burls on your first build. They look fantastic, but are hard as shite to work with.
Hope this helps a little bit. I am sure Wez and Johnathan will have more to say on the matter and more to add. :)