2002 Jeep Liberty Sport, 3.7L 4WD – rear window not latching and intrusion alarm not working

Discovered your YouTube videos a few years back, subscribed, and I love ‘em.

Got a weird problem.

While fixing a hood un-latching problem, I removed the battery for a few days or so. When the hood-latch job was done and all was reassembled, I found that the rear window wouldn’t latch shut. Subsequently, I noticed that the intrusion alarm wouldn't set. These two phenomena are probably related. My Chilton’s manual doesn’t even mention either the rear window or the alarm system.

Side note: Prior to that job, I had fixed a leaking drain problem of the sunroof, and had the right-front floor rug pulled back to drain out the water and dry out the rug and the foam that’s under it (which took about a week). Considered right-front seat removal, but didn’t do it, so I did not disconnect the electrical connectors under the seat. And I didn’t notice any connectors that had been under water (only wires).

Got any insights on these two problems (rear window not latching and intrusion alarm not working)?

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All my carriage returns went away when I copied my write-up from Word 2007 to here, and hit the Submit button. Do I need to use line-feeds instead of carriage returns?