I have done a guitar for a mate of mine.
Remove electrics and neck.
Sand it down to the undercoat, try to leave the undercoat on, if you go to the grain of the wood it will look naff. Fill any dings with a compound such as a car body filler, I used one that is OK to use on wood, can't remember what it was called. Once filled, sand smooth again.
Mask anything you dont want to spray paint and hang the body up so you can spray all the way round. Put on lots of very thin coats of paint, maybe 10 or 15 coats, if you put it on really thin, it wont run. Build the colour up slowly and be very patient.
Then put on lots of varnish coats, another 10 or 20 very thin coats.
use some t-cut scratch remover to polish it up like glass.