When you run the motor so that it lowers the roof all the down, what position is this plate in? Is it somewhere in the middle, or is it all the way at one end or the other?
I'm thinking you may have run the motor up part way and therefore moved the plate when you originally reattached the cable for the roof to the spool. Seems like you need to detach the cable, run the motor all the way down to the bottom position and reattach the cable. See what that does for you.
And thank you for the pictures. They are helpful on this end.