I did what you recommended and the roof is in the down position and not leaking. Removing the motor and moving the cables with a screw driver worked well. I did not get it lowered under it's own power. I cheated and moved the cables one at a time to lower it into place. As soon as the weather warms up I'll finish that piece.

Is there any way to tell if the teeth on the motor are still OK? There is no obvious sign that there is something wrong, but there is not much there to mesh. When I did get everything back together and tried it under power there was some movement and then grinding. It appeared to me that I may have put the glass back in and it was not fully seated in the frame. I reseated everything and then just lowered it manually to where it sits now.