Josh,
I by no means am the most qualified to help you with this, but I think there are a few "commonly" answered questions that could do you some good.
First if your claim that the foam blocks seem to be deteriorated, I can only assume that you are speaking of the foam that is glassed over inside the deck that holds the pylons to the boat. Are the loose, or does the foam look messy. I cant speak for newer boats but my old '74 is a wreck inside, I guess Hobie figured no one would see them, they dont need to look good, so what might look like breakdown could just be a mess of fiberglass and foam. If they are actually broken down, you would be better off finding a newer boat, or if someone can chime in to help you fix that problem, to me that seems like too much trouble because you would need to access the insides of your hulls, which is at the least is an installation of a hull port near each pylon which could weaken the structural integrity of the hull??
As far as your idea with re glassing the entire boat, way too much effort for common problems. If you search the post you will find tons of blister repair stuff, which usually results in sanding the blister down, patching the resin with polyester resin (if you plan to gel-coat) and then paint/gel the fixed area. It has been advised many times in the board that painting the boat adds a lot of weight to the boat which can cause performance problems such as pitch poling. If you have to redo the hulls, I would recommend you patch what you need too, sand and gel coat (if you can handle the amount of work). Others have sanded, and used paint like interlux brightsides. If your boat is white, you shouldnt have much problems matching the gel for repairs. Rick Buchanan just wrote an article about re gel-coating the boat in the Hobie Hotline you can get it here:
https://www.hcanamembers.com/PayDues.aspx Pay to get a printed copy or...
http://www.hobiecat.com/hobieclass/ to get a .pdf
Adding another layer of glass will make the boat very heavy which you might end up regretting. Spot repairs of blisters on white hulls and small cracks in the gel-coat aren't a big deal, if you have colored hulls its going to be hard if not near impossible to match the color.
To me it sounds like your biggest problem is potentially the broken foam in the deck.
Luke[/url]