You had mentioned in an earlier post about the noise behind drivers shoulder, I am assuming the "bad" side is the drivers side.
Look at part labeled 21 in diagram, it is a plastic cover attaching to the glide rail.
It connects via two tabs that slide over the glide rail, you can either just slide off to remove and see if that may be the issue of them binding on the glide rail when closing.
When replacing my transmission and cables for the top I did not have one side correctly attached and it did bind a bit preventing top complete closure of the clam shell.
Takes quite a bit of force to bend the clam shell permanently as they are made to be flexible.
Good luck