Hi and welcome mate! =)
Firstly, Iīd put the single coil aside for the moment and just match it to whatever else you choose (though you should have a look at the Irish Tour, Slowhand, and Trilogie, as one of those is likely to arise, but more on that later).
Main problem here is that even just saying "I want to play Vai things" is a huuuuuge range. I mean how many signature pickups does that man have now?
Also, important here, what is your amp like?
Assuming it is at least partially modern in tone I am inclined to suggest the Emerald neck, Holy Diver bridge for now. The HD is one of the classic 80s hotrodded PAF types. Naturally you think Holy Diver type sounds and a lot of mid 80s or so stuff. It however is pretty versatile and also my top recommendation for early Dream Theater and such. Added bonus is that it also does pretty well with leads as it has a very musical tone to it, so a harmonics loaded screaming solo with that should work well.
The EM neck meanwhile is a glorious cross of modern and vintage. Modern wire for definition, attack, and cut, while having vintage sweetness from the AIV magnet. Fluid as heck. Seeing as both these players seem to sway between vintage and modern pickups but put a ton of weight on their fluid and rounded tone this seems like a great option. Pairs extremely well with the HD bridge as well.
One other thing I might suggest if your guitar feels on the bright end of the spectrum is a look at the bridge Crawler. That, to me, might be the best one to capture the general Story of the Light vibe, especially Gravity Storm.
With either of those combos perhaps the Irish Tour or Slowhand are best options for a single. Irish tour being a classic SC (+) with added mids, bottom, slightly less top end, and some sort of rock dust that makes it come alive under gain in a different way. Back the volume up and it becomes darn vintage again too. the Slowhand sorta does the same thing, but takes it a step further.
