Looks good! I built a transparent kayak once, too, and I'm making another right now. I'd have to agree that maybe the heavier gauge clear vinyl might have been a better choice. In any case, the stuff is a lot tougher than it seems - I think Tom Yost has transparent-skinned boats that have been around for 3 years or so, and are still going strong.

You might try a heat gun on your wrinkled cockpit area, which I have found will remove some small wrinkles. Be careful not to cook the vinyl too much, which ultimately makes it pretty brittle. Experiment on some scraps!

I really like the the shape of your boat, and all the knee and leg room! How does it roll? Have you experienced any fogging up of the interior while you are paddling?