I have a lot of the same concerns myself. All I know about this is what I've pieced together. But the my info is sketchy at best.
Here's a plan:
Get a cheap hunk of acceptable tonewood, cut out the rough guitar shape. Screw on a cheap piece of 1/4-1/2" unfigured maple or something, router the neck pocket and pickups, throw together a quick and dirty guitar and record a bunch of tones from clean to dirty, and jot down playing impressions.
Unscrew the top, router out some cavities like the warmoth mentioned above, repeat the playing impressions. Then continue to router away wood, recording sound and impressions with each pass.
It seems like a little extra work and expense, but in the long run, you may avoid a blotched attempt, and get a much more dialed in result on the first attempt, which is what we all want, right? You may even be able to get wood that is blemished, checked or otherwise substandard from a supplied at a discounted brice.
Any thoughts on this?
-Sven