Fix rear window, goes opposite direction as others and car thinks it's a 4 door car when it's a 2 door after battery had died?

Car battery died, jumped it off. And back passenger window goes opposite when pushing and go up. Goes up when I pull long bar for all 4 windows to go down . But all other windows go down. Also dash shows a display of car with both back doors open but my car is a 2 door. Out side mirrors and dash stay on thinking doors are still open. Also sunroof opens but when pulling top opener it does nothing and my truck won't open. I can hear it try but don't. I believe it's due to thinking it's a 4 door not 2 door hardtop convertible. I know that some computer needs to reset/ reflash / but recode. And have a good mechanic that has a ICON computer. But it performed with hexagon coding and bits . We were told and tried to change the third or fourth bit to the proper code I think it was an 11 when it was a 13 or something like that but I'm wondering can do you know the right steps to take through the icon and right codes for the bits and numbers to put in to the right s parts or where to check to see if something is thrown off or to do anything to help that. Or not using that going a different route how to fix this. The car is still drivable with all that aside but I need two new front tires went to discount to get my tires and my tire lug to unlock my tires is in my trunk my trunk won't open. Please help Thanks for your time it's much needed.