North American Motoring - Issue with both windows

Hi guys, I should have listened......but I did't. I installed an aftermarket thermostat and housing on my wifes 08 clubman, even after reading on here that there are problems with them. I did for 2 reasons, it broke an hr from the dealer and I didn't want to rent a car to go get the part, and it was a little cheaper at advance auto and I could walk there. Well short story it spilled it's guts an hr from home in a doctors office. Wife was in the car and shut it down but didn't take the fob out of ignition slot. Naturally lights stayed on and killed the battery, key wouldn't come out and couldn't get it in neutral. Plastic pull under shift boot was already broke off. Finally put on cables and got it in neutral and flatbedded it home, rented car went to dealer bought proper housing and installed it. Now one would think my world is all rosey and one would be wrong. To my question, the windows roll down a bit when you open doors and rollup automatically when door is shut, but now mine won't roll up! Anyone out there know how to reprogramme them to shut. I assume it happened because of low battery voltage. Thanks all

Walt