windows and top won't work after trans replaced

As a first step check the fuses under the hood and the dash and make sure they have power to them.

Check fuses at left end of dashboard. Check for communication with the comfort and roof modules with a full function scanner. Common problem is water getting under the carpet and corroding the comfort module and/or wiring. Remove door sill trim and lift carpet to access plastic box just in front of drivers seat. Open box pull comfort module and disconnect harness to inspect for corrosion. Follow harness forward looking for corrosion. There are multiple wire solder joints that can corrode causing loss of power to the comfort module that controls the windows, alarm, interior light, and other convenience items.