The new white ones are alder and MII. The original and one and only Evo is alder and was one of the protos for that line. The painted floral that you are referring to is Evo II which came after Evo and has a sustainer in it, but yes the florals were basswood and FWIW, he also thought the cloth added to the tone.
He sounds like Vai no matter what wood the guitar is made of or what pickups are in it, having owned mulitple JEMs I personally like the basswood ones myself, I prefer the rootbeers and PBKs because I like my guitars a little more subtle. I have owned the white and blue alder ones and they sound good, although the Evo pickups aren't my favorite. Of course, I really dislike almost all/especially white guitars with gold hardware (IMHO if it ain't a LPC, don't put gold on it, notable exception being a Richie Kotzen tele because when you are that good...).
And, to tie it back to the original post, basswood is a good tone wood, just need to find the right pickups, and I would not have chosen either of the Duncans you tried. The PATB distortion has too much midrange and a chopped treble, works much better in a brighter wood like ash.
