While everything Dougc84 said above is correct, for most of his career Trey has used his old Mesa MK3 from like 1986 or something. 2x 212 cabinets, both homemade. You could just get by with a single 212.
I would start by finding a clean Mesa MK3 profile, bump the mids a bunch. Put a Green Scream in both stomps 1 and 2, with the first one set to mid gain, and the second one set to full scream (use your ears...it might be less than full on the KPA). Then add a compressor in stomp 3 (Trey runs his compressor AFTER his OD's) and adjust it for fairly heavy compression for early period Phish, less compression for more current tones.
Use your volume knob a lot.
That's should get you close, but his guitar is is also a big part of his sound. A semi-hollow like a 335 should be pretty close sounding.
To be honest, I haven;t had much luck getting a great Trey sound with my KPA, but I don't have any Mesa profiles either.
Let us know how it goes!