I learned how to build guitars when I was a teenager. Designing guitars is a lot like making patterns for clothes, first you figure out the neck scale and then you can go wild. Some parts have measurements you have to follow so the instrument can be tuned and play in key. That is the neck length and the distance from the neck to the bridge.
The body for an electric can be shaped like anything but remember you might need to have a case for it to fit in. Custom cases are so expensive.
The body shape is traced on heavy card board, with the electronic cavities and the neck joint and bridge placement. The pattern is placed on wood cut on a band saw and shaped with power or hand tools.
There is a lot of sanding 80 to 600 at least ten coats of lacquer and a lot of buffing. I think it took 6 weeks to build.
This guitar has been my main guitar, it's been in recording studios on stage, in photos and I never get tired of it.
DO not try this unless the guitar you are using is one you dont care much about. Dont do this to your main guitar, or one that has alot of value. Save that for the pros. This will explain some basics to customizing the body of your guitar, by yourself. You need to be able to paint, in whatever way you want to do it. Some use spraypaint, and some use brushes. I think the best approach is the AirBrush that they use to paint tshirts with.