You did read the book, "Make Your Own Electric Guitar" didn't you? If not I'd recommend you buying it.. it answered tons of my questions.. and made me think about alot of stuff I would have overlooked.. such as Scale Length, Number of Frets, neck dimension, body shape, what kind of neck join:bolt on, set, or straight through?, bridge height, neck angle, headstock angle, head shape, body thickness, wood you'll use, pickup and control selection, nut width, truss rod(what kind?), control mounting(pickguard etc. etc.), binding, inlays, countouring, fretwire size, and finishing you will use... all must be decided before you build... Hope you have already done all the planning.. Good Luck on your project
Matt