As for the black album, James said he used the Mark IV on the demos, but in other interviews he said he used the same Mark II C+ he'd used on the previous couple of albums for actual tracking. He used it in conjunction with an ADA MP-1 preamp somehow, I wish I knew the specifics.
I've been trying for the black album rhythm sound for years, as it's my favorite guitar sound of all time. Puppets, Justice, etc. get all the attention in terms of guitar sounds, but to me the distortion on Black is just so smooth and huge. I can get close with my Mark IV, as it's easy to ALMOST nail that sound, but there's still just a little something missing--it's trickier than it seems.
James also always used a studio-quality parametric EQ to shape the sound, though I'm not sure if that was instead of the Boogie's graphic EQ or in addition to it. I assume he needed to pull out specific frequencies that weren't on the Boogie's graphic. They also used around 8(!) mics for that sound. I don't know anything about the processing.