I was just "Googling" this the other day while thinking about painting my hardtop. Here is what I found, hope it helps you:
(1) Cover surface areas with protective covering to
avoid paint damage and extra clean-up time.
(2) Using a razor knife, slide the blade between
the quarter glass and the inboard edge of the reveal
(3) Cut around the interior perimeter of the reveal
molding and sever the cap of the reveal molding.
23 - 64 STATIONARY GLASS TJ
(4) Using a cold knife, cut the urethane around the
perimeter of the quarter glass.
(5) Remove the quarter glass from the opening
(Fig. 1) .
(1) Trim the urethane from the quarter glass opening
fence. Leave a 3 mm (0.1 in.) level base of urethane
on the quarter glass opening fence.
(2) Place replacement quarter glass into quarter
glass opening and position glass in the center of the
opening against fence.
(3) Verify the glass lays evenly against the fence at
the sides, top and bottom of the replacement quarter
glass. Next, make alignment marks on glass and top
with a grease pencil.
(4) Remove replacement quarter glass from opening.
(5) Position the quarter glass inside up on a suitable
WARNING: DO NOT USE SOLVENT BASED GLASS
CLEANER TO CLEAN QUARTER GLASS BEFORE
APPLYING GLASS PREP AND PRIMER. POOR
ADHESION CAN RESULT.
(6) Clean inside of quarter glass with ammonia
based glass cleaner and lint-free cloth.
(7) Clean the outer edge of the window glass with
naphtha or a similar product.
(8) Apply molding to perimeter of quarter glass.
The butt weld of the molding should be centered at
the bottom edge of the quarter glass.
(9) Apply Glass Prep adhesion promoter 25 mm (1
in.) wide around perimeter of the quarter glass and
wipe with clean/dry lint-free cloth until no streaks
(10) Apply Glass Primer 25 mm (1 in.) wide
around perimeter of quarter glass. Allow at least
three minutes drying time.
(11) Apply Pinchweld primer 15 mm (.75 in.) wide
around the quarter glass fence. Allow at least three
minutes drying time.
(12) Apply a 10 mm (0.4 in.) diameter bead of urethane
to the center of the quarter glass fence surface
CAUTION: Be prepared to install the quarter glass
immediately after applying the adhesive. The adhesive
begins to cure within 10-15 minutes.
(13) Align the quarter glass with the grease pencil
marks and position quarter glass on fence.
(14) Push the quarter glass inward until the
reveal molding is seated on the hardtop. Use care to
avoid excessive squeeze-out of adhesive.
(15) Open windows and liftgate to prevent pressure
build-up while the urethane is curing.
(16) Apply 150 mm (6 in.) lengths of 50 mm (2 in.)
masking tape spaced 250 mm (10 in.) apart to hold
quarter glass in place until urethane cures.
(17) After urethane has cured, remove tape strips
and water test quarter glass to verify repair.
Here is the link to where this info is from:
Help! Hard Top side window removal - JeepForum.com