I won't be of much help but I too am a phan and really dig Gordos style. He keeps it very groovy while the band is heavy on improv jams. I'd suggest incorporating a lot of different techniques in your style. He uses a pick frequently I'm pretty sure, not exclusively... A lot of his sound has to do with the sweet, phat and synthy tones he gets from his rig and effects.
To figure out the bass parts to a song like YEM you might want to figure out the roots and changes of each part first, and play along with it a lot to know the different parts the bass is doing in each section. Sometimes it may serve as the rhythm or it may a take a melody role, there are bass solos and fills all over those compilations too.
Here's a link to some Phish bass tabs. http://www.strangedesign.org/chords/index.php
You can google his rig, and these guys were talking about it. Mike Gordon's Gear for the Phish Reunion