Do you have only one FOB? Do both Fobs fail to unlock the car? I would also clear all the codes you have found using the scan tool.
First thing to try is disconnect the battery for about 1 minute. This will reset many of the programed systems in the car. Reconnect the battery and maybe it will correct your FOB problem. Also wouldn't hurt a thing to check every fuse under the hood. Failing that I would remove the cowl under the windshield and disconnect the siren. The batteries within the siren can leak and contaminate the circuit board in the siren's anti-theft system causing all kinds of problems.
You can also download the service manual for free here on this website ( there is a link to another website) and the entire electrical system is laid out for you. service manual
Have you tried to re program your FOB? click here; program key
PS. The car will drive fine with the siren disconnected. My siren on the Limited has been disconnected for years with no problems. You just won't get an audio alarm.