Joel, after looking at the lexan options here in town, we are going to secure the stock windows in place using the metal channel the bottom of the window sits in. They will only be used for transport as well. From what we measure, you need about a .180 thickness of lexan to fill the window channel and not flop around. I could only find lexan .09 or .220 at HD and lowes had .17, but it was their standard plexiglass, and not the lexan. IIRC they had the same thickness lexan as HD did. I am afraid if the window does not fit snug in the channel, the wind going down the road will allow it to flex and pop out of the channel. You can flex the lexan with a heatgun, you will need some wood clamps.
FYI, We got our toyo stickers this week in the mail, so if you haven't gotten yours, you might want to call them.