Weird... is there any possibility that the distributor sensor wires were flipped in the process? Any module (HEI or otherwise) triggers off of a + going edge from the reluctor, which is the leading edge of the reluctor pulse if all is set up right. If the wires get flipped, then the module will trigger off of the trailing edge, which will make the actual timing vary all over the map. That would explain the big change in timing.
Regardless, that was a vexing problem; you get a lot of credit for the persistence to figure this out.