You're pulling out some old ones today!
Don't worry about the windows. Finish the kit without them, then get your self a bottle of Micro Kristal Klear from Microscale. (about $2 most hobby shops have it and if not Squadron) With small windows like that it's a breeze to make them. You dip a tooth pick in the Kristal Klear and run it around the edge of the window so the entire frame has some on it, then holding the toothpick parallel to the fuselage, touch it to one side of the window frame and draw a bubble across the opening to the other side. The bubble will dry clear. If you mess up, wipe it off with a damp paper towel and start again. The finished "window" will be more clear than the plastic one you lost.