The scale length of a guitar is actually the string length. Simply measuring from the playing side of the string nut to the break over point of the string on the bridge will give you the scale. Usually though we'd measure to the 12th fret (half scale) and double this number, as strings usually intonate a little longer than actual scale (has to do with action height and the distance the string is depressed when fretting, amongst other things).
If you are building a custom guitar you may choose from the three scales we offer and our standard bodies will accept these necks perfectly, just the same as if you put them on a Strat body. Easy, huh?