Since there are silicones that are tank safe and some that aren't, I wouldn't use anything that you don't know for sure are fish safe. You can still use the windshields but I'd get some fish safe silicone to make a hinge with.
Green algae is a result of enough nutrients and light so you may need to reduce your light hours and/or decrease the nutrients.
As for replacing glass, just make sure the old silicone is really cleaned out so that you have a clean surface to use a solid bead of silicone on the repair. Do not rush the post repair test. Let the silicone sit and cure for at least the amount of time on the directions. The longer you wait, the better. Some manufacturers use clamps to secure the panels while some just use a masking or duct tape to secure the panels. What I've done in the past is use the moldings as a guide. Once the silicone has been applied and the panels are secured in place, replace the top molding to ensure the repair is correctly positioned.
Hope this helps.