Anti-theft preventing vehicle from starting

The battery died on my vehicle. So when I charged battery the alarm will not turn off and car will not start. The passenger side door was making a funny noise so I replaced the actuator. Now door works fine, but the back hatch is not reading right. Sometimes it will say open when it is closed and closed when it is open. I also reset the key and alarm shut off but the battery died. So I tried resetting again but to no avail. Please help, out of options.