Help! I jammed my top transmissions?

[CharlesE]

Well I pulled the right side transmission and re aligned the gear and everything was working until the end of the cycle the clamshell got stuck down again.

After popping the clips off and inspecting the transmissions this time the left one now isn't moving. I'm ready to get a shop or the dealer to fix it for me at this point. I'm Wondering if a dealership would be able to re-allign it.

[CharlesE]

Does anyone have any idea why the top works perfectly putting it back up but putting it down the motor doesn't stop when the clamshell closes and it locks itself down?
It stops the motor when putting the top up but the light doesn't turn off going down and the clamshell does push down the switch.