[DanEC]

If I remember right - his build used an aluminum block also. Could be a few hundreds of an inch difference in crank flange to rear block machined surface distance than original Ford. A few hundreds more flywheel thickness. Quicktime bellhousing overall depth could be slightly different than stock Ford. Lots of tolerances that could go a little this way or that way - or all in one direction.

I don't remember ever spinning a transmission from the rear wheels. Makes sense it would feel a little different in gear. I think in neutral the countershaft and gears are primarily turning only. In gear it's picking up the input shaft and the clutch disks may be lightly touching on the clutch plates as they spin because they haven't been fully seated in. I know that putting a new bearing retainer on a Muncie there is a lot of drag on the input shaft before installing. After it's been run a little bit the input shaft is back to wobbling around as loose as a goose because of the front ball race bearing. But, really need to check the back disk plate for any damage.