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?
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