Sounds like you need to do a lot more reading. Get Melvyn Hiscock's book and read it through several times
The amount of frets doesn't make any difference to how you route the neck cavity, just buy the neck and make a template based on that. The bridge position is the most important thing, obviously it needs to be 25.5" away from the nut.
Not sure what you mean about the difference between a string through cut and tremolo cut?? They are completely different, and every bridge will need to be mounted in a different way. Buy your hardware first and you'll know what you're dealing with.