Here's a little write up in regards to rear liftgate window hinge replacements on my 2001 TJ according to several sources including the TJ 2001-2006 Service Manual. Please feel free add/correct as needed, I just figured someone else may benefit/save time from this information:
-Torque wrench able to measure Inch/lbs
. and not foot/lbs.
-Philips screw driver
-Flat head screw driver
-Replacement Hinge(s), note: drivers left and passengers right hinges have different bolt lengths so order appropriately as the left is shorter and the right which is longer goes threw the wiper motor (if you have one). Please note I bought mine via ebay but there re numerous other vendors who sell them as well. (No part numbers, sorry).
-Rubber O-ring (should come with the hinge) unless ordering a complete kit which will have additional parts and rings.
Open up the window to a 90 degree level and use saw horses (if available) to keep the window up(if your hardtop is one the ground like mine which is easier to work on IMO).
Loosen up the bolt on the inside glass first on the drivers side, then work your way to the hardtop bolts afterwards. Pay attention to how the plastic and rubber gaskets on the hinge are placed
. You will need to put it back in proper order on the replacement. Once the replacement is in place, start with the window bolt and place the nut back on by hand first and then using a torque wrench and proper socket size, torque up to 53in/lbs
(again not in feet, double check). Then torque up the two bolts that attach to the hardtop to 95in/lbs
**Warning: Over torquing can result in broken glass so please double check.
Remove wiper motor cover using phillips screw driver (watch out for falling screws, lost one in the grass so make use of a tarp under). Repeat same process for wiper motor/passenger side as you have just done for the drivers side.
Here's an example of hinges gone wrong:
Attachment 284929 Attachment 284930
And the replacements, and to remove those stains, I used Vim with bleach (kitchen cleaner product) and scrub pad/water(repeat as many times as needed but took me 3x to get the window properly clean):