Tim has recommended PKs for Vai tones. The EVOs are ceramic, so this makes sense. I use a C-Bomb and PK in my JEM77FP, and I love how it sounds. Nails Vai tones, but with it's own character. The EVOs were too dull and had a muddy quality with chords for my tastes. They are all a little hot for Satch sounds but amp adjustments and effects play a big role in shaping that tone. Cold Sweets also do pretty well. Notice I'm aiming at all the ceramic pickups!
Satch solos sound great with CS neck pickup, and I'd imagine so would the Aftermath neck. Vai, again mostly uses ceramic neck pickups, and has a more hot and compressed sound than Satriani. There are other possible options with the vintage hot pickups, but I honestly would stick with PKs or the C-Bomb/PK combo. DiMarzios are pretty bright but less open sounding than BKPs, so either set would be a huge improvement in dynamics, clarity, and overall character.