I ran into a similar problem with a project, quite awhile
ago. I bought a NOS body from a Fender HMT bass on
ebay and assembled it with a neck from a '51 RI. Looked
and felt great, but would not intonate. It was driving me
knuts, so I broke down and asked a professional. Turns
out I was using a 20-fret neck on a body that was designed
for 22 frets! Both are of course 34" scale necks, but it had
more to do with the length of the neck pocket and the
mounting placement of the bridge.....mostly the bridge. The
HMT having a fixed bridge, remounting the bridge was not
an option. I could have shimmed the neck pocket (ie built
a 1/2" spacer to push the neck farther forward). But now the
mounting holes would have to be redrilled, etc.
The simple fix was that I used another neck, from a 22-fret
model. There are plenty of used necks on ebay and it just
required some patience. I snagged a neck from a "Cowpoke"
P and....viola! Bolted right up, intonates perfectly, and even after
5 years is still my main squeeze.
Just offering a different opinion, based on my experience. Perhaps
a different neck would solve your problem and allow you to have
your project fulfilled? BTW, once I learned all this, I can easily
spot a 22-fret neck on ebay....it'll be the one with 4 dots after the
12th fret instead of 3 (duh me!
