here is what knowledge i have about the wood, it does have an effect on the tone of the instrument. i read a book on building electrics when i first started building and it had a short segment on wood types in the back which i have found to be pretty accurate. as a general rule woods like alder and maple (and i think ash though i have never used it) are going to have a really bright sound, like a tele or something. mahogany is a little darker sounding and will bring out the mids a good deal. walnut has a very dark low sound to it, but it works well as body wings for a neck through guitar (have used it for that on a couple). i personally like maple bodies a lot, though they are really heavy, they are really aggressive and punchy sounding.
as far as neck joints go i prefer a neck through, it can be a little more difficult, but i think that it results in a more stable and better sounding guitar with greater sustain and playability (this is because you don't get the bulky neck joint so the high frets are much easier to reach). i don't think there is much difference between a bolt on or a set neck as long as it is a good tight fit. if given the choice i would do a bolt on over a set neck cause if anything ever goes wrong then you can take it apart easily. with either of them the fit ought to be tight enough that when you put the neck in the pocket there should be enough friction to more or less hold up the guitar. there another style called a neck tennon, but i dont know much about it though, i have never made one.
i have never made a hollow body either, and I'm not really sure the benefits of semi hollow bodies or chambered hollow bodies appart from making it more light weight and possibly giving it a little more volume unplugged. i know the reason the went to complete solid bodies way back when was because of feedback issues with hollow bodies though.
hope this helps some. also, that is some sweet lookin wood, ought to make a couple nice guit-fiddles
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