The secrete is to . . .
start a hole thru the sealant and then thread a heavy fishing line thru the hole. Wrap each end of the line around something stout, put someone on each end of the line and saw thru the sealant all the way around the window. The window will pop right out. You still have to clean ALL of the sealant off the boat or the new sealant won't seal properly and will probably leak.You may also want to consider plexiglass instead of lexan. Plexiglass is stiffer and will span a greater distance for the same thickness, and is harder and more scratch resistant.The best sealant for rebedding the windows is probably Dow 795. It is used by most boat builders for bedding windows, and is used in skyscrapers to hold and seal plate glass windows. Its designed to withstand hurricane strength winds, and is still flexible enough to allow movement of the windows during expansion and contraction due to heat cycles.Good luck with your project!