Sounds like you'd prefer an alnico magnet pickup for a more natural sound.
I've listened to all the tracks in your list just now. I think a nailbomb would suit very well the dirty Prodigy style, but I'm not sure that it fits to the Rick Rubin stuff. The guitars on those tracks are quite layered with other sounds, but they sound a bit more vintagey to me.
The E2 is a very cool guitar, but I don't have much experience with the walnut/maple laminated construction and how it would affect tone. Generally in the more uncertain cases its better to aim for more low output, to get something that would work first time.
What pickups are in the E2 - is it the original Dirty Fingers (they have double rows of screw pole pieces)? How are you getting on with those?