Temp Fix
I took the window (port) out and took a good look at it and the opening it came out of. Considering my objective and alternatives I decided to do a temporary fix that may even be the final solution. First I caulked the small space between the cabin exterior and the inside shell of the boat so if there is a leak it will not get between the two. Next I took the glass out by spliting the aluminum case that holds them together (careful here, the top and bottom and left/right are different,slightly, make everything with felt tip pen). I then wire brushed everything, even sanded some. Then I reassembled everything dry to see how it went together. Next I purchased a tube (that fits in a gun) of latex caulk (color or clear, your choice). Then took it all apart and put one glass in at a time, using plenty of caulk. The channels are larger than the glass is thick so I made some wood shims to hold the glass in place overnight. Next day, I did the other glass and assembled the thing and cleaned up excess after it skined up. I then pushed the port in place (right side up)dry to see how things fit (important). Took port back out....Then I sanded and caulked the outside edge of the opening(didn't put enough on the first time, took off and redid) and pushed the port in place, wiped up the excess (should be excess squeezed out all around if you used enough). I went inside to look at how every thing fit there because you can see daylight around the port you may need to touch up with caulk from the inside before you put on the inside trim and tighten everything down (the i/s trim pulls the port into place). The inside trim must be rightside up and be sure the screw holes align (flashlight needed) before putting the first one in.I don't think it will leak.