Mechanic F*ed up
Automatic's use pressure and need pumps, not the M5OD-R1 transmission.
And nothing about the M5OD was a bad design(well shift rail plugs, were marginal, lol), there are literally millions of these transmissions still running fine today, they were in fact a very good design.
So the noise only happens when output shaft is moving, so when truck is moving.
I don't think a u-joint would "squeal", "clunk" is the usually description for u-joint.
And rear axle problem would sound far enough away to not be described as transmission noise.
And coasting in Neutral it still makes the noise?
I would think you would be better off to get a used M5OD-R1 from another 2WD 3.0l Ranger.
Parts list for M5OD, no "pump": http://www.therangerstation.com/tech...KoygoMazda.pdf