Neck pocket woes - sand the body or the neck??

I forgot about neck pocket height...thankfully I have a functioning Charvel so I can pull the neck off and compare all those specs when I get the Fender neck in. (Body is the same model as the one I already have!).

Yeah, fit the pocket to the neck. There are exceptions. You can do a visual inspection of the neck heel and see if there are some really goofy things that could be fixed. Usually this isn't much more than finish too thick and kinda lumpy, which will interrupt an otherwise nice flat surface. You need to be prepared to polish/buff it out if it is going to be in a visible area.

Definitely be checking that neck angle, too. I don't know the old Charvel stuff well enough to say for sure, but it could end up with a very weird neck angle. The real old Charvels were Boogie Bodies (now Warmoth) and presumably will be anchored in Fender spec pretty well, but after that I just can't advise.

I would also measure the scale. Lay the neck over where it would go, measure the nut to the 12th fret (you can just mark on a stick if you want) and then compare that measurement from the 12th fret to the bridge. It SHOULD land towards the front of the throw on the saddle intonation screws. If the bass was designed for a 24 fret neck or something then this will never work out, afraid to say. Confirming the scale length is part of this, but it isn't the whole story, it plays into the whole proportions of the instrument. If the original was designed with a longer neck and shorter body then the math just won't work.