I know that this is going to sound pretentious as fuck, but in my opinion, Adam Jones' tone is more about an idea than the particulars. His live rig has been unchanged for years, but his studio rig is always changing. He usually records with whatever happens to be lying around the studio space, and mixes up the amps differently at different points of a song to get a desired effect. It's not about WHAT he records with, but HOW he records it that really gives you the Adam Jones sound.
So don't get too caught up on the particulars. What's most important is that you use two different amps into two different cab IRs, panned hard left and right. That massive stereo spread is essential for replicating his tone. Above and beyond that, play around with different high gain amps with relatively low gain settings, layer them and see how it sounds.
As far as amps go, regardless of what he actually uses, I've had the best luck replicating his style of sound using these amps:
RECTO2 RED MDN - Run the MV high, gain low, and EQ bright with a clean boost in front of it, so it's pretty percussive and mid-rangey.
HERBIE CH2+ - Run it fairly flat in the EQ, but put a Peak EQ filter between the amp and cab to replicate the "mid-cut" function.
SPAWN NITROUS - Dial out almost all of the base and gain and run a clean boost in front of it. This model has the perfect chunkiness on the bottom end and gives you a bit of more of that midrange. It also plays very nicely with pretty much any amp you pair with it.
Anyway, that's my take on it. Your mileage may vary. Good luck.