My rear window wont close. Hits the latch but wont catch. This happened when
battery went completely dead. Any help will be appreciated.

Have you driven it? (even with the window open) Once you go over (I think) 18 mph the doors should automatically lock and that will actuate the rear window latch. You may also try fiddling around with the remote release and remote door locks to see if it will catch then.

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2005 CRD Limited Flame Red w/ Renegade rock rails & light bar, AirLift 1000. 225/75R16 MT/R's on cheap black steel wheels, dual MOPAR subwoofers, Ipod kit & seat covers, Samco hoses - totaled and gone. 2008 WK Laredo 3.0L diesel - AirLift 1000, wife won't let me mess with it much. 2013 JK Sahara on order.

This started happening to me a few months ago. I sprayed the entire mechanism thoroughly with WD-40, then moved the latch into the proper position by hand, then shut the glass a few times to work in the lube.

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2005 Stone White KJ Limited CRD 4x4
Off-Road Pkg
Trac-Lok
Emu 790s/948s
Skyjacker H7088s rear/Bilsteins front
15x7 Black Rock Lobos/31x10.50 Firestones
GDE HOT Tune + TCM Tune
Euro TC
CB radio
Thrush Turbo muffler
AEM DryFlow filter