1996 Explorer Limited Alarm Issue

[nmdag]

1996 Explorer XLT V6 4WD

Situation:
Digging around in the rear left panel cavity in the trunk/bed where the tire iron and jackstand are located, there's a junction box back in there with two 16 (I think, could be 8, can't recall off the top of my head) pin connectors and an audio cable. I had to unplug these things to get at some stuff that was jammed up in the cavity. I just plugged them back in when I was done thinking that there would be no problem. Now, if I start the vehicle up the alarm sounds and won't shut off until I unplug the top connector.

What I've done as a temporary remedy is leave the top connector unplugged. Only problem is this triggers something else that makes the red THEFT light come on on the dash if it's in Park or Drive without the engine running, which makes it so that I can't start the vehicle, so to park it I just put it in R and set the parking brake. To start it up again I have to put it back up to P and turn the ignition. Big hassle.

Is there any specific way I have to/can reset the alarm system or fix this otherwise?

I've searched around here and not found too much, but my google-fu skills may be lacking. One thing I've read is to disconnect the positive battery lead, leave the door open, turn the key in the ignition to ON and reconnect the cable. Will that work or am I being trolled? Local Ford dealership is closed at the moment.

edit- other temporary solution includes removing
Alarm Disarm DARK GREEN/VIOLET (-) DRIVER'S KICK PANEL
and grounding it to disable the alarm completely, however, I'm not looking to do that. I need a reset or something. Or maybe if I plug the connectors back up in a certain order.

edit 2- I should mention that this model has keyless entry.

edit 3- It appears that "these things" were connectors for what is apparently the alarm module (the box in the left rear panel). What I'm going to try is disconnect the battery, plug the alarm module back in, and reconnect the battery. Will update later with results and pictures.

 

[nmdag]

Problem was solved in the most obvious way possible. I was too annoyed by the noise of the alarm going off (these suckers are loud) to think straight apparently.

Plugging in the alarm modules activated the alarm as usual, then simply unlocking the driver side door with the key (manually) shut it off. Either my key fob's batteries died at a rather inconvenient time or the button doesn't work to shut it off under my circumstances. Will probably get a new battery for the fob tomorrow.

Now I have no problem except for the $1700 I just sunk into the transmission and the $500 I'm going to have to spend on the suspension. And the $150 idle air control unit that was making an annoying whine which has been replaced.

Next on the list is an interior detail and get the clear coat on my hood fixed. Does anyone know if the paint/clear coat used on the hood is different from the rest of the body? My car was owned in a rather sunny city which wrecked the clear coat on the hood and the small strip of metal between the hood and the windshield but left the rest of the body, including the roof, alone.