Recently the factory security system has been going off on my truck for no reason..and only when it rains. I was thinking that it might be a low charge on my battery since it is the original...but I am not sure. My biggest fear is that I am begining to have computer issues. Any suggestions or does anyone know how to trouble shhot?

your alarm has no sensors other than door pins, unless it has been upgraded with something aftermarket. Have a basic electrical system test done. Voltage test, battery load test, and verify alternator output. If that checks out and the problem persists, the dealer can check the computer. It is possible that a door latch is bad which contains the domelight/door trigger switch.

ETA: rain setting alarm off is usually indicative of a hood or trunk switch, on your factory setup, there is no hood switch, the trunk is in the liftgate latch.