You may have done this already but the manual says the following:
After each of the following operations are performed, reset the limit
switch (with built-in motor).
I Regulator removal and installation
I Removal of motor from regulator
I Operation of regulator as a single unit
I Door glass removal and installation
I Glass run removal and installation
After installing parts, proceed as follows:
1. Close the door window completely.
2. Press the reset switch and open the door window completely.
3. Release the reset switch. After making sure the reset switch
has returned to the original position, close the door window
4. The limit switch is now reset.
Be sure to manually open or close the door