I haven't operated the lynx at the RCA museum in a couple years, but Idon't remember it being that loud.
4th gear is straight thru the input to output shaft, so the countershaft is not being used. So your noise is likey the countershaft. One thing I have noticed on the last couple ford transmissions I opened is that the thrust washers get eaten up. I suspect the culprit is the modern oils, which are not yellow metal friendly.
But even without wear, you are turning the counter shaft, and as well have the input and output shafts turning at different speeds in all gears but 4th. That means the bearing in the input shaft is working, as are the two larger bearings at input and output as they will now have some extra side load on them.
Of all the vehicles to have this happen on, the lynx would have to be one of the worst. Even trying to look into that transmission is a pain, and there isn't much you can do to it without pulling the engine.
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