Live he uses an Alembic preamp... cant remember which... into a QSC poweramp and 3 Eden 410XLT cabs on top of 3 Eden 210XLT (could be 210T) cabs.
In the studio he's used a few different setups.
He's done the Ampeg 8-10 tuibe rig (Core), and then I think he moved on to a split signal involving a Marshal Plexi guitar amp run dirty and an Ampeg (?) Keyboard speaker cab run clean. (Purple, Tiny Music...)
I think the last setup is what you are looking for info on.
On the later recordings he started using a Sansamp bass driver to add some more grind to the sound. (No. 4, Shangriladida)
I bought the issue of Bass Player where they had the info, but I left it with my parents in Miami. In that issue they said he uses 3 - Eden 212XLT cabs under the 410XLTs live but from seeing him live and on video I know thats not the case.
Ive had some pretty good sucess getting a similar signal by running my main rig (Eden preamp with Eden 210SXT cabs) clean and flat, and my combo amp (Eden-Nemesis 210 combo) on top of it with the mids boosted around 1-2kHz and the gain cranked so that it distorts when I dig in and the compresser on.
Peace
Nick