Repair finished, as of 4am last night.
My final analysis is that this damage was the intersection of 2 events. The first was the short water pump (factory part number 21110aa026) was installed, when the longer one was needed. Somehow, I missed the visible 5mm offset on the pulleys the first time around. The second event was that when I replaced the studs with bolts, as I had seen work successfully in other threads here, I kept the torque on the bolts and lockwashers equivalent to the FSM torque for the nuts. This didn't completely engage the lockwashers, and when the pulley had additional side forces put on it by being out of position, I imagine that they walked out quickly and destroyed themselves.
Solving this without replacing the water pump with the long factory unit, as a time and money issue, was a matter of installing longer studs, placing a stack of three 1.5mm thick washers on the studs beneath the new pulley, then reassembling. The annoyance was finding the correct automotive studs and trimming them to fit. I went through 3 sets of studs before I got the ones that would engage correctly.
M6x1.00x30mm with the unthreaded shoulder in the center, are 1mm too short overall after being trimmed to fit the pump side, and cant fully engage the nuts.
M6x1.00x40mm with the wide, offset, unthreaded shoulder look perfect after trimming to fit, but the unthreaded should sticks out above the surface of the fan clutch by .5mm, preventing nuts from clamping parts.
M6x1.00x37.5mm is the answer, with a much shorter offset unthreaded shoulder. Fit is correct for WP side, and after trimming the long side to fit, they allow firm torque on both ends, and don't hit anything. You can get them from Tacoma Screw.
I'll give it another couple weeks to make sure stuff holds the way it should, but I think this one is done.