Crazy, my '99 4Runner with the R150F 5 speed has made that whining since I bought it with 151k.
I bought the Marlin 1200 lbs clutch kit, replaced the clutch, pilot bearing, throwout bearing, flywheel, shifter seat, resealed rear main and replaced seal, replaced T-case, trans, and axle fluids.
The vehicle now shifts great, but alas that noise is still there. I was thinking input shaft bearing after doing some research, but the fact that you replaced yours and it didn't fix it makes it extra puzzling.....
