So... I think I need some help here PLEASE

I have a well maintained 2006 H3. It has a Viper alarm with a bypass of the GM Passlock and stock alarm.

Last year my sunroof drains weren't draining and I was getting a build up of water, so i had to pump out the sun roof drains. Last night we had a large rainfall and I feel some rain got in again.

When I opened the door to get into my vehicle, the dinging bell went off constantly as if there was a key in the ignition. I wondered wtf? Then I put my key in the ignition at it started....only to immediately turn off, so I tried this several more times and it did the same. Starts then within a couple seconds turns off. I came inside googled the issue, and everything points to GM Passlock. So I went back out, touched the carpet on the passenger side and closer to the firewall it is wet. Not drenched but obviously some water came down the A drain. (these drains drive me crazy btw)....anyway, I figured that i would outsmart the system and start it with the remote start, which i did and I put the key in, turned it to on, pushed the break and my truck stayed on, and I drove with it. Not far but around the block. All the while the Theft-Deterrent light stayed on. So I parked on in front of my house. Shut her down, and tried to start her without the Viper Autostart.....and she works....so i am thinking..... OK.....maybe I fixed her..... but NO .... I exit, turn on the VIPER alarm, and start walking away. Then all the lights flash, the VIPER alarm goes off, the stock alarm which is not supposed to be attached starts honking and all mayhem breaks lose! FML. I go back to my truck, use the VIPER unlock to stop both alarms for going off. I sit in my truck a little bewildered of whats going on and all the interior lights start flashing on the dashboard and then all remain of momentarily, so I try to arm the VIPER and both alarms go off again. I disarm, and then try start the truck manually and it turns over but doesnt start. Then I try start it with the autostart and again it turns over but doesnt start. So again, I try to lock it up so I can deal with it tomorrow and all the lights start flashing on and off for about 1 minute, just as I was going to disconnect the battery it stopped. I entered the vehicle, tried to start it again, there is def power, it tries to start but no success whatsoever. I then locked the VIPER alarm solo and it worked, so what I have noticed is that both the VIPER and the stock THEFT - Deterrent are activated.

Anyone have any ideas. I am hoping its just a water issue as we have brutal rain in Vancity and **** happens everytime I park under trees during major rainfall. Let me know please. Your help is greatly appreciated.