Diesel dog,
Sounds like a cool engine swap you have planned ! I hope you keep us informed of your progress. IMO, engine swappers with a good plan rank toward the pinnacle of mechanicdom !
I rebuild my own auto trannies (GM only, so far) and can mostly 2nd PEH's opinion. An Automatic will primarily have some of it's bushings ruined if towed...similar to running an engine without oil pressure. It seems like a standard tranny should still get enough lube, but it does seem possible to me, that on a long tow, the output shaft bearings or seal on the tranny may have been damaged or maybe failed simply from old age. Let us know what you find out.

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Diesel-guy