Sounds odd.
A GM frame is a GM frame.
Only suggestion I can give is to make sure that the car is on a level flat surface
when first fitting the top.
While I never had a top that did not fit in, I often encounter ones where it is difficult to line up all four bolts if the car is not level.
The new weather strip may also be causing your difficulty as it would certainly be thicker when new and not compressing completely.
You might also lay the two roofs carefully onto each other, frame to frame to confirm that they are identical in every dimension. They certainly should be.
Pretty silly answer from Ecklers after buying a $1500.00 item.
Keep us updated with your findings and results.
Marty