I've got the same vibration you're describing. Only really noticeable when I rev it pretty good before I shift. My tach isn't working so I cant tell you what RPM. I have a 3.4 out of a 2000 4Runner with R151F trans in my 88. Resurfaced OEM flywheel, OEM Aisin clutch and Koyo TO bearing.
If you have no vibration revving the engine, it's not an out of balance issue with anything rotating. It would vibrate regardless of stepping on the pedal.
The pedal only "feels" the connection of the fork and TO bearing and that would be transferred through fluid in the line. I was also thinking the clutch fingers may not all be perfectly aligned with each other causing a type of chatter when you step on the clutch causing that pulsating feeling into the pedal.
The TO bearing touches those fingers and if even one was sticking up just a little it could cause it. Kind of like dragging a stick across a chain link fence. Maybe the edges of the fingers have a rolled up edge from being stamped out or sheered when manufactured. But................you tried another clutch. Maybe a not so good TO bearing?
I have put plenty of miles on mine with no problems. Shifts great, no constant vibes driving it, no metal being generated in trans so I'm not pulling it. Too much work for a slight pedal buzz at high revs. I don't really notice it unless I really tach it up between shifts.
If you can't stand it and pull it apart again, post up what you found.
