The way to go about this is to clamp the neck in, install the bridge and tail piece, sit the pups in the cavities and grab a length of string...
Run the string from the bridge to the headstock and this will give you an indication of string clearance over the frets and pups.
(There is is thread somewhere here on set ups that should answer all your questions)
String height over the pups should be between 1-3 mm, depending on how hard you play..