Rhino..... I'm right there with ya bud! I've been throwing design ideas around in my head for months now. I have several I want to try, but I am way too busy with paying work to get to them yet.
I am a professional seamstress/fabricator/patternmaker ect ;D I make marine canvas and do a lot of millitary equipment where I work. (I cover 53 foot hellicopters. LOL )
I see a lot of crossover between marine and auto. Heatsealing is best for sure, but sewn doesn't always mean it will leak. We don't even own a heatsealer (though we are looking) and our windows don't leak. I would suggest you use seam tape in your seams it helps to seal the stitch. There are also some silicone products made just for that purpose.
If you want to get real fancy, check out Tendra thread from Gore. Its about $100 or more a spool wholesale but its guaranteed for life to never rot. You can also look for waterprof zippers (used mostly for wetsuits) by ykk. I use them for our millitary work and I plan on using them for some of my "reworked" top projects.
For basic suggestions I recomend using a heavy duty industrial walking foot sewing machine. Home machines will not do what you want. Trust me on this.
Headers are for sure your hardest part. I would suggest getting them from besttop, unless you really want to experiment a lot.
I haven't been able to do much because of time constraints, but I have over 20 years experience in marine canvas. I can't wait to hear what you come up with. If you have any questions or want to bounce ideas, I'm game anytime. I'll try to get someting done soon. I want to rework my supertop a bit. I'll post what I've done if I ever get time to do it. (Not looking good in the near furture