Not sure what he plays now, but back in the day (early-mid 90s?) it looked like he was playing a modded 70s style Strat. Floyd Rose, locking nut, and a humbucker in the bridge, through a Marshall. Effects, I dont know. Definitely a wah in there though.
Im going from (hazy) memory from the 3 times I saw Primus live. I could be dead on, or way off!