Originally Posted by Twangysteel
is there a stable way to shim the length of the neck?
and also how much trouble am I going to have intonating this thing after all is said and done?.
You don't need to shim the length of the neck. There are thousands of basses out there with a gap at the neck heel. The pickguard covers it, so it goes unnoticed.
For your intonation, measure from the 12th fret (doesn't have to be there, but it's an easy point to reference on both necks) to the heel of the neck. Do that on both necks.
If you get the same measurement, your replacement neck will intonate. Live with the gaps where the rounded neck heel butts the square body, OR make or get a custom pickguard made to fit the rounded neck heel instead of the square neck pocket.