Sometimes the dowels get misplaced and the trans gets installed without the dowels in place, using only the bolts to align the trans input shaft. As the bolts are typically a slip fit, the possibility of misalignment and wear to the convertor and pump can occur.
The dowels are beefy 1/2" steel pins that are pressed into the trans bell housing flange and usually remain there when the trans is separated from the engine. If the dowels are not in place, the minor misalignment could cause the knocking/scuffing you are hearing loading one side of the pump or stator. Elongated convertor mounting holes in the flexplate can have the same effect.
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