Not sure how it would slide in the track (wouldn't track need to be twice as long as the welting?), seems to be too rigid to compress. What you could do is put that in and attach waterproof zippers to the rubber/plastic part (the welting).
Quick search for waterproof zippers yielded
http://www.tizip.com/
Best of luck, looks awesome!!!
One last thing, kind of too late, but why not lexan for the sliding windows? more expensive than plexiglass, but way cheaper, stronger and lighter than glass. Also having double track and 2 panes of glass/lexan would let you tint one and not the other so you can get the sun block when needed (obviously each piece would slide separately).
Maybe you can still do 2 panes on the sliding: one glass and one lexan, and tint one of them. You can put lexan on the outside/inside depending on where u think it will scratch less. I am pretty sure you can tint lexan that will hide the possible yellowing (some lexan i have seen has been guaranteed for many years not to yellow).
G