Every Studebaker engine and transmission is aligned and dowel pinned at the factory. The dowel pins were missing from previous work done on this engine. Yep! You never know what you'll find --or not find-- when you work on a car that's sat for 20 years.
Brad checked the alignment and used oversize pins to hold the center line of both crankshaft and transmission. These have to be on the same plane or the flex-plate will crack and/or break and the front pump of the transmission will wear out or break.