I'm no expert on the tech stuff, but putting these questions into a new thread in the Tech forum as opposed to Pickups forum will probably get you a lot of answers. However, if PhilKing recommends replacing as much of the electronics as possible, I 100% believe in his recommendations.
As for Trey's guitar, I don't think he's got a lot of clever onboard electronics (like Jerry Garcia with those signal buffers and things): individual volume controls, possibly only a single tone control?, and a fairly standard 3-way pickup selector switch. I think his koa guitar has a bronze saddle and bone nut.
What Trey does have is a fairly complicated "post-guitar" set up, with different effects units and paths (famously, he uses 2 tubescreamers in sequence to color relatively clean amp sounds). I think his main amps for a while have been modded vintage Fender Deluxe Reverbs; he's also had (maybe still has) a signal split think with the signal going off through a preamp to a Leslie or something like that. It's been about a million years since I've seen Trey live (Phish played the UK like once, maybe twice, since I moved here, and Trey certainly hasn't brought any of his solo bands over!) so I'm not really sure what his rig is like these days! These are issues for the Gear forum .... :)
But his guitar (other than being a custom-made hollowbody) is pretty straight-up in terms of kit. Someone oughta sell him Mules, 'cause they gotta be better than the Schallers! :)