I feel like if you all practiced more you could get the sound you want out of the current VH4's...
The first time I saw Tool, his Blueface took a shit on the opening song and he used the Silverface for the rest of the night... His tone was still godly.
So just experiment with the settings a little? I understand the old Bluefaces have a certain mystique to them, but frankly if you want the Adam Jones tone in a box, then you'd need an amp that blends both the Marshall Superbass/lead and his Diezel... which is honestly kind of a cool idea for a single amp. But in the mean time, just run some hot humbuckers on a 24.75" scale length guitar with 10-52's into channel 3 of the VH4, mess around with the gain and the EQ some (he loves his mids and he runs the gain as hot as possible before it gets muddy). Play it loud enough for the police to come knocking (he plays loud, like dumb dumb dumbass loud; apparently even when they practice at the loft, he plays loud). Diezel's sound great at low volumes, but they have their own way of coming alive at the stadium levels he plays at. I guarantee you if Tool started today, Jones would sound just as good with what's available to an up-and-coming musician. It's not
what he's playing, it's
what he hears in what he's playing.
There's an EQ for a reason, you should mess around with it more. You might even find some of that trademarked
darkness if you do...
If you're still craving something then make sure you're running
all of your effects into the front end. He doesn't use the loops on the amps. The Marshall is responsible for the brightness, but he's been known to use an EQ for a treble boost. He uses his wah pretty frequently but he applies it subtly; he cocks it or slowly sweeps it for a lot of solo's or to create dynamics. Outside of the dual amp out-of-phase setup, imo his flanger has the largest effect on his tone. It gives it that "morphing" texture it has. Run the rate and resonance really low, and then alter to taste. He's used a lot of different settings over the years, but they've all been consistently on the subtler side.
Truthfully, I don't believe anybody has the definite guide to his tone. I don't even think he does lol. He's got such a monster tone that's been refined over decades of experimenting. He's not stopping lol. He is semi-consistent with a few things: he uses the Les Paul's (sometimes the Flying V now; essentially nice guitars with humbuckers), the modded Marshall SuperBass(SuperLead specs) + the Dual Rec during the early period or the VH4 in the latter period. But everything else? Exact settings and models get changed regularly. The third amp was a dual rec, then it was a VH4, then it was a Knucklehead, now it's a VH4. The flanger was a BF-2, now it's a BF-3. He used a Line 6 DL4, and he's used a BOSS DD.
Just experiment guys! Experiment and practice! I've always felt like instead of copying tones, you should try and create a tone that gives you the same feeling.
