The wrong size alignment rings could be as truckernix described: all 216 rings and pre-1950 235 rings are smaller diameter (the alignment rings might have been correctly stock-listed as 1941-1949 235 rings).

That is an understandable mistake and an easy fix.

The mis-fit of the manifolds (together and to the block) is more difficult to understand. The two manifolds bolt together in a different plane from the downdraft manifolds (as shown in the picture-link). That should not affect the relative alignment of the two manifolds to the head.

Grasping at straws: finding up-draft manifolds is a challenge. Perhaps the manifold assembly (or, just the intake manifold) is from a pre-1950 updraft-manifold engine? What are the casting codes on the manifolds? Compare them to the codes listed in Group 3.265 in the Master Parts Catalog.