So are you going to remove the aftermarket alarm? I don't get why anyone would bother installing aftermarket unless the OEM alarm was faulty and they were looking for an easy solution. Hopefully you can get everything back to original. Good luck.
Just wondering if you've checked the grounds in the harness. I used to have the drawings, I think its A1. This particular ground wire which has an attachement point under the glove box and above the knee bolster is responsible for your entire HVAC system. On my '96, this wire was pulled out of the clip. When I restored it, no flashy flashy, blower worked fine and my dash lights all worked again.
If you unlock the doors, the car will lock itself again unless you open a door. This is a timer built into the relay. This may be a clue for you. Do your interior lights come on when you open the driver's door? If not, the relay may time out and lock. There could be an issue with the driver's door lock module. Otherwise, I would remove and inspect the door lock switches on the driver and passenger door. Loose wires, screws, dirty switches are all potential culprits.
I had this problem. Found out I didn't fully torque 1 bolt for the lower control arm to the frame bushing. I got 3/4 of a turn on the right side rear bolt. Noise was gone.
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