Drivers Side Water leak and random passive security system engaged

These subjects both occurred in the same weekend during torrential rains. Here is what I discovered for those who have a similar vehicle:
Swamped drives side carpet: Below the Power Steering unit are two drain holes. They were plugged by a massive amount of debris. I removed the debris and sealed the seam where that area meets the fire wall. So far so good. This is a very easy check, if you cant see two drain holes on a quick look (flashlight may be needed) then reach down and start pulling out the needles, leaves etc; if this area is clear, then remove the door panel and check for moisture. The other area that should be inspected is below the windshield. You will need to remove wiper motor to access the entire front area (5 screws, very easy). There areas on each side and in the center where water does tend to pool.

Random Alarm:
My first intro to this was horn honking when doors were opened or closed - horn timed to dome light on and off (delayed dome light off on with passenger door) then two days later, lights flashing and car stereo blaring. Twice in one night.
There are multiple threads on this topic and it appears to be one of many Jeep weaknesses. I luckily found no severed wires in the door boot, but did find the boot was not secured and several wires have cracked insulation. The section from the drivers side is supposed to fit over the boot from the door side keep all the wires comfy and dry. It was not sealed in my case, so rain water from the drives door moulding was pouring right into it. BTW, securing that boot is impossible ( I still cant do it) possible due to the age of my car (22+ years) so my trashy duct tape fix will have to do for now.