With the clutch out the pilot bearing should be sitting still in relation to the motor and trans, in gear or not. Seems to me that should rule it out unless the noise shows up only with the clutch pushed in. Same thing with the throwout bearing for the most part, tho it can freewheel a little with the clutch out. Seems really odd to have two trannies do similar things, I keep thinking things like I wonder if the motor/trans is lined up right. That would stress the input shaft and cause whine/wear in the bearings. It should also be eating up the pilot bearing pretty fast too though.
If the pup had been sitting for quite a while it could just be wear showing up from bearings that had run dry or something. That doesn't account for the 4spd going in similar ways though. If it did sit a while, it would be worth getting it good and warm and changing the fluid. Might be some stuck on gunk that has come loose with newfound activity.
I guess I don't really have much of an answer, but maybe this gives you something more to think about. The trans in my 77 2WD has whined fairly loud under load in 3rd gear since I put it together some 14-15 years ago. Never has gotten any worse. Changing the fluid often does help, and if you are not in a really cold climate you could give it 90W. I've had a trans that was run with it for years before I got the truck and it didn't seem to suffer any ill effects. Never know though, so I've just stuck to the recommended 30W motor oil.
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