94 Bonneville alarm system

I just recently removed the carpet and padding from my bonneville, because of a huge leak. When I removed the carpet I noticed some loose wires coming from the alarm system above the fuse box. When i messed with the wires the alarm went off. I've had this car for a few months now and the alarm has never worked. After the water dried up I looked at the loose wires that have been cut and the alarm diagram says they go too door locks, horn grounds etc. But most of the wires are connected. I cant get the alarm system to work now. I also noticed on both sides of the car there is a rectangular shaped black thing with wires running to them. The black thing has a cap on it and the metal is very corroded I messed with those wires and heard a clicking noise. I suspect they go to the door locks because the one on the drivers side is the one that makes it do the clicking noise somewhere in the car, and when i turn the car off and open the drivers side door the stereo will not turn off but it will with the passenger side door. Does anybody know anything about the alarm and how to connect the loose wires or anything about that mysterious black box?