Ok, I think I understand what happened.
The lips on the rear of the receiver didn't fit into the grooves on the rear trunnion, correct? So the rear of the receiver is bowed out, making it too wide for the top cover, correct?
This is common on these '65s and '63s. Your problem is that the grooves are too high for the receiver, they need to be widened (and lowered). What I did was I took a dremel with a cutting blade, and carefully went over the bottom portion of the rear trunnion lips, making it a little bit wider. I only needed about a millimeter or so, go slow, do a little, and test fit. Cut a little more, test fit, repeat as necessary.
When you put the rear trunnion in, look at it from the rear, you can see where it needs to be widened in that slot.
Hope that helps...