Below are my notes from when I replaced all my rubber window channels.
Good luck. This isn't difficult but it takes a while and gets tedious.
Replaced all the window weather stripping. In total, I used 3 96-inch long pieces of StanPro p/n AS1528 (75000638) for the vertical strips. Used 16 72-inch long pieces of p/n AS1369 (75000486) for the horizontal pieces. All pieces are continuous.
-- I ordered the weather stripping from CR Laurence Co. via::
Glass Distributors
3800 Kenilworth Ave
Bladensburg MD 20710
-- the top and the bottom of the aft windows are 55" long
-- the vertical pieces of the aft windows are 33"
-- the top of the forward window is 40"; the bottom is 71"
-- the forward vertical piece of the forward window is 28"
-- the aft vertical piece of the forward window is 25"
The process:
-- remove the vertical metal strips (that are attached to the glass) by pounding them loose with a block of wood and a hammer
-- pull out the weather stripping from the top channels
-- lift the windows up and swing outward -- do not need to remove the vertical brace
-- remove the lower and vertical weather stripping
-- clean the lower channels with a wire wheel, alcohol, Scotchbrite pad, etc.
-- vacuum with a piece of tubing taped onto the vacuum hose
-- clean the windows with a razor blade
-- clean the vertical metal strips by scraping with a small screwdriver and scrubbing with 409
-- replace the lower & vertical weather stripping
-- cut out strips in the bottom for the window channel drains
-- smear Vaseline on the upper weather stripping channel
-- replace the inner window; install the vertical metal strip using white Life Caulk as adhesive
-- work the upper weather stripping into place by holding it in place and sliding the window
-- hammer the metal strip in place with a block of wood and a small hammer
-- repeat for the outer window
I put ProSeal on several places on the port window channel. One spot near the aft end of the forward window had a bubble in the weld that looked deep. I also used ProSeal on the forward angle (about 15" back from the forward end), in the forward corner of the forward window, and in the forward corner of the aft port window.
I did not extend the weather stripping all the way aft under the black lexan piece -- it does nothing. I sealed the bottom of the lexan panels with black 5200.