Chris, if the window flexes, you're going to have a devil of a time getting it to seal. If it were me, and it's not, I'd replace the plexi with the stock thickness and strength. You can obviously reuse the gasket material. In the long run, this may be the best and cheapest solution. In the future, replacing the floor is going to be a PITA because water intrusion is not a good thing!
Ten Forward - 2014 Escape 5.0 TA
Double Yolk - 1988 16' Scamp Deluxe