While your at it drill some 1/2"- 3/4" drain holes in the bottom near where the old ones were. Remember you will be fastening the bottom to the body sill too so make space for all. I drilled and riveted but spot weld would be nice...whatever approach to get it done. Rivets. I knocked out the steel shank after pressing a bit then hit them flat with a hammer. Rivet, Spot weld, weld, epoxy...it'll all work. I would put this lapped joint on the bottom when I drill some drain holes. The top of the window rubber seals and the bottom, I think is designed to drain out the gap made by the disk/shims at the bottom sill. Drain holes need to be clear of where shims and their fastening screws will be. This is a good time to dry fit the metal to double check your fit...before you cut the rubber
I would recommend using a new long razor knife, the razor type about 1/2" wide that you can break off 1/4" bits at a time. I didn't have one so I used a new single edge blade in hand and after making a mark where the two ends will meet. A good technic is to hold the sides of the rubber firm, channels up, and chop straight down to cut. I chose to make a diagonal splice because this will give more surface area for a strong end to end bond and bears less of a chance sliding widow and debris will catch the edge.
Cut one side first then, lay that cut over the other side, scribe with a pencil and carefully chop cut the other side. I did have to shave a bit more off to make the cut faces align. Think before you cut and make surely sure that the rubber is fitted down into the metal corners, no slack before cutting.
I super glue gel the ends in sections because you'll never get the whole thing in one go and muckle it. What I mean is that there are a lot of profiles to meet together and glue successfully, no screw-ups. Glue in sections. I used a scrap piece of the angle metal to support and hold while pinching ends together. Carefully take it off the scrap metal before it dries too much. Once dried well, fit the rubber and metal together. The metal, rubber and windows come out and go in as one unit. A bit of a juggle so more hands help. The small lip that keeps the windows from falling out becomes tighter when the shims are fitted. Once the shims are fitted underneath the possibility of the windows popping out are gone, the gap is closed. Mind you these measurements were for my Patrol, you may want to make shims of different thickness to dial in the fit.
The shims need to be a stiff non corrosive plastic or...at least 3/4" so it makes a flat platform for the rubber and metal AND windows. I slipped the shims in after I put window unit in. The shims should be about 1/8". I sealed old holes and drilled new ones in the bodys sill and used #4 x 5/8" phillips heads through shims. I have not yet but stops are maybe overkill except if you push so hard you tear the rubber. The stops are just pieces of rubber with a #4 screw through them that act as a bumper stop for the window. When you simulate the square cornered window hitting the round radius corner of the window frame you'll see their possible usefulness.
BTW, I could not wait for paint and realized that I can just spot prime with rust converter and install NOW and remove for paint later. BTW, a tad of contact cement on the inside cab inner seal will help when the real install happens. FINI



