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[breezernate]

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I have a vibration in my 98 T100 4x4 manual shift 3.4 liter.  I was told by previous owner it was throwout bearing...I can't believe it.  It only happens under acceleration with clutch engaged.

Driveshaft u joints and center support bearing are all new.  Drive shaft recently balanced.

Toyota tech told me input shaft bearing to transfer case has a noisy/worn bearing.  I can hear kind of a gritty bearing at 40 mph or so, but not too bad.  Considering swapping out my VF1A tranfer case to see if it goes away.  Doesn't happen with rear drive shaft removed when in 4WD, so could also be a rearend problem?

[Rocksurfer]

Sure, could be a loose pinion nut that is allowing the pinion to float around a little. It will cause the pinion to hit the carrier creating a slight vibration and growl as the pinion gear rolls along the carrier.

[breezernate]

Pinion nut is tight on my truck...I checked.

Companion flange at transfer case, however, seems slopply.  Even after tightening nut to 120 ft-lbs it seems not as tight as it should.  It comes off by hand after removing nut...no puller required.  The rear companion flange to the rear diff took a puller to remove.