UPDATE
So, I replaced the upper tranny mount (the one near the battery) and the rattle is absolutely and completely gone. It's even better than before the rattle began. The whole thing is super quiet...almost too quiet. That might be because I had added DynaMat in the meantime. The steering column rattled a bit at first, but only when coming to a stop. I adjusted the freeplay in the clutch, idle speed, and max fuel to what I believe is correct all around, and now the steering column rattle is gone, too. I have no tach, but the idle sounds pretty relaxed, so I'm thinking it's okay. I basically increased idle speed until the idle was right at the point where the motor smoothed out, then turned it ever so slightly higher. Adjusted max fuel so that it smoked black and then turned it back a quarter turn. Adjusted freeplay in clutch per Bentley. I have some new (well, remanufactured) injectors to install this weekend. I'm hoping it gets rid of the smoke (as I smoke at all max fuel levels and all gears and speeds except cruising in 5th on the freeway...and I'm sure I smoke a bit then, too, but it's light enough to be invisible to me). I also have mounts for the other mounting points, but will replace those when I replace the pump and timing belt.
Did I do anything the wrong way? Should I have calibrated idle and max fuel differently?