Hmm aye, seems you have some good ideas in mind there.
The PAF's Sound better in mahogany bodied guitars to me, so I personally would probably go for EVOs.
That's crap lol. I PERSONALLY would go for tone zones for a darker sound lol, but yeah EVOS for the satch and Vai stuff
Seing as how you're doing up a satch guitar you're going to have some Satchabillity in the JS100
SO I'd just take that PAF-PRO out, Whack it in the JS's neck, and don't bother with a joe, you'll save some money lol

, then Install some evos in your other axe for a different flavour.
Hope that helps man,
Spike.