Yeah, don't do anything further with it. Something's misaligned, and if you try to force the issue something's going to break.
Sorry to ask you again, but I'm not totally following your description. What is moving from one side only? The top or the metal cover on the back? And are you saying that the passenger side of the cover goes lower than flush with the trunk lid when closing? If so, that's definitely strange. If you mean that the top is moving farther forward on one side than the other side, that makes some sense if things are out of alignment.
If things aren't moving in sync and the motor sounds like it's straining to move things then don't try anymore. If you're able to leave the top closed, light on or not, do so. Send a message to 1schoir on here. He doesn't come on very frequently, but if he does and sees your issue, I'm sure he'll be able to give you some good advice on what to do. Just try to explain what's happening as clearly as possible and supply some pictures if you can if they will help.
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-O/D
1997 Arctic Silver Boxster, 5-spd
IMSR + RMS
Robbins glass window top
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