All of the items you mention are controlled by your car's Body Control Module (BCM) and such malfunctions frequently occur when the settings are disrupted especially after a dead battery or a battery replacement. You can reset the BCM by disconnecting the car battery's negative (ground) cable for 30 minutes. After 30 minutes, reconnect the battery cable, start the car normally and allow it to idle for 10 minutes without touching any controls (lights, radio, temperature/fan controls, etc.). NOTE: you may experience a rough idle until the BCM calibrates the throttle body idle air/fuel mixture. After idling for 10 minutes, take your car for a drive where you can accelerate to a speed above 40 mph for at least 30 seconds. Then slow down to a speed below 35mph for a few seconds and then once again accelerate above 40 mph. Repeat this cycle at least three times total which will enable the BCM to recalibrate your throttle body's operating parameters and your transmission's shifting points. Once you return home, allow your car to continue idling while testing your windows, lights, etc. and hopefully everything will work properly. NOTE: do not be alarmed if your "check engine" warning light illuminates as this is normal when the BCM loses data input from the battery being disconnected. It's also common for the "air bag" warning light to illuminate as well. Both warning lights should go out once the BCM senses all is well which can take anywhere from a minute to a week.My 2004 Chev Malibu LS no longer has back up lights, the locks don't work & the transfer case with the 3 speed in low does not work. Also the resume button doesn't work. I'm not sure if they are related but seem to have seem to have started at the same time. Does any one have any fixes, especially for the back up lights?
If this doesn't fix your problems, your BCM likely needs to be reprogrammed or replaced. Both procedures normally have to be performed by a GM dealer unless you can find a repair shop that has the necessary equipment to reprogram your existing BCM or to program a new one.