The Jag schematic I have, (and
Duncan has) shows that upper tone pot as being 50k, which would be terrible for a spin-a-split. The simple solution is to use the 1-meg volume pot instead.
The pot to tap the humbucker shouldn't affect the tone in any appreciable way
if you use a 1-meg pot, as stated above.
I wouldn't use the upper pot for neck volume. It'll just open a new can-'o-worms. Other than that, I think your ideas are great. Should turn out nice.
I'll mod that diagram for you if you aren't in a big rush. I've got several in front of you.
Artie