Yes, glad you have it figured out. The 1/4" discrepancy you described would not be due to a mismatch of V8 and 4 Cyl parts. Fwiw the 4 cyl drive shaft and torque tubes are shorter than V8s. the 4 cyl engine in a 33/34 has to come back further than the v8, so the trans mount is reversible to sit the trans further rearward, consequently the torque tube is shorter.
The clamshell nuts should be a 5/8 af. Ford used a lot of these, 7/16 unf normally (these days, anyway) being 11/16. Save any 5/8 af 7/16 nuts you may find when dismantling any old Ford. In the clamshell situation that extra clearance is helpful.
Mart.