I believe the sewing machines used for hypalon are the type that could sew a quarter panel back on to a pickup truck after a bad night of four wheeling. I would get some quotes from pontoon makers maybe the originator first, then one of the small pontoon makers in OR for instance. If you get sticker shock and decide to go for it maybe a good tent stitcher with kevlar thread and aquaseal applied liberally would get you through several seasons (?) Aquaseal patches usually outlast the general fabric of my waders.
My pontoon boat has an internal bladder... making it a structural problem verses and airtight challenge. Not sure what yours has but obviously one poses a greater challenge than the other. Good luck with it!
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