I did an extensive search and could not find anything that was like what I am experiencing, so I’m asking for advice....

I went to put my top up for winter storage, forgetting my tonneau cover was still in place.
I hit the up button, heard it torque hard and I stopped, reversing it back into the full down position. That was weird...
Did that sequence twice before doing giving myself a dope slap for leaving the tonneau cover on.
The second time I did it I heard a small chattering from the drivers side rear.
These tops make noise all the time and I pray every time I open it anyways, so the noise was not all that unusual.
After the tonneau cover was off, the top went up and down but would not latch properly. I tried it 3 times, getting it to work once, with the noise happening intermittently.
On the 4th try, the top still closed, did not latch, the drivers side was now a little higher than the passenger side, and my noise seemed louder.
It did not want to retract then.
I stopped....
Something is now out of alignment or possibly broken.
I first popped the rear side covers and checked the 19mm bolts. They were nice and tight, and I didn’t see anything loose, broken, or missing in the linkage and bows. I don’t think there is a problem here unless it’s an alignment issue due to torquing with the tonneau in place?
I then figured that maybe the drivers side drive cable had gotten too short and had slipped a little when it torqued, so I pulled that out from the motor side cable housing for a peek.
It came out easily without protest and I see no evidence of slipping or damage.
Both cable ends look good, but no matter how I tweak the cable and housing, I now can’t get either cable end to engage back into the transmission when I try to put it back together.
It seems like maybe something is out of alignment or galled because the square cable end should just slide back in, right?
Can I pull the cable housing from the transmission without removing the transmission?
It seems very loose like it should pop out, but I don’t want to break it.
I read about these drive cables getting short over time but I cannot find the thread on how to tell when it is too short and how much they should stick out.
Is the quick fix just to cut the cable housing in half, make it a little shorter, and then sleeve it with a rubber hose so more cable now sticks out the ends?

Where should I go now, and or can anyone please direct me to a helpful thread? I’m stumped.
I do not want to go with a manual or semi manual fix at this time. I would like to get it working properly.
Thanks in advance.