I swapped a 282 Getrag into my 89 Sunbird last week, and when re-installing the top trans mount, the bracket was 2" out of line.
To get it bolted up I had to loosen the rear engine mount and pry the whole engine and trans back...somethings not right there.

I have read that 3rd gen J's have a difference between auto-manual engine mounting brackets, what about 1st and 2nd gens?

You switched from Automatic to Manual, correct?
If so, yes, they are different and you should not try to drive your car until you get the correct one installed.

Yes, i did change from automatic to manual but the donor car is gone to the crusher two days ago, the only bracket i removed was for the trans because it was snowing when i went for the parts.
Back to hunting down more parts eh,,,the joy of swapping to manual.

There are 4. Front of the block, rear of the block, under the rear mount (to the body), and the upper trans bracket. All of them are different.