the lads are spot on with evrything here, especially the spalt issue - stay well away untill you have a few guitars built. Even then it can be a nightmare to work if you get the wrong piece that just want to fight you at every turn.
I would recomend sepelle, mahogany, alder, basswood or ash to start. All nice timbers & not too hard to work. Poplar is nice aslo but can have a fluffy edging when worked that can be offputting & ruins the build for early builders. Stay away from cedar, it can break too easily if cut wrong.
If you do try make a neck, get a pre radiused & slotted fretboard from stewart mcdonald. make sure the grain in the neck timber is bolt straight - or close to it.
If you dont have templates yet them PM me. I will need your email address to send you some CAD & pdf drawings of RG, JEM & Universe guitars. Also strats, teles & les pauls as these will most likly be the basis for all of your setting out of hardware.
A doner guitar is a good idea. just make sure you dont go too cheap on the hardware, $30.00 trems are a big no for example. get a fender or gotoh hardtail bridge, much cheaper than you would think.
If you like I can have a look around here & see what is lurking in the dead guitar pile. I know I have a neck from an Ibanez S model, Im not sure what else I have.
Anyway - good luck, enjoy - & make sure you ask lots of questions & put up lots of photos