#1
I took off the neck to my student model and the neck to a nameless V (it had to come off anyway, there was some warping going on) and come to find that the holes for the screws are of different distances.

lesson learned for the n00b

I still want to build my frankentar, and I still want a 25 inch scale neck.
The two concerns I have now are intonation (how will I find it and keep it)
My other concern is the screw holes for the neck. If I were to get a virgin neck (that is with no holes), so long as I dont turn it into swiss cheese, it should maintain its shape, right?

Finally! What should l do from this point?
#2
to find your intonation, you have to measure from the 12th fret to the nut, then try to equal it from the 12th fret to your bridge. this means a lot of adjusting.
yours truly, the bastard under your bed