Welcome to the tribe!
There are several threads regarding 22-2 projects in the Rebuilds Forum you can refer to for answers. Among them are current projects "1971 Flatback" and "new 222 rebuild". These guys are going the whole route with their boats so there likely aren't any questions you can stump them on. As you dig into the forum more and spend some time studying various project boats you'll pick up a good education regarding ways of going about replacing decking and evaluating the stringers.
If this is your first rebuild, my suggestion is to put the Sawzall down and spend a few evenings reading what others have done. I can practically guarantee your time spent doing so will save you both labor and money.
Regarding the 6" x 6" blocks used to core the deck, there are a couple theories about that. One theory holds that by using the small blocks the deck core could be cambered easily in the mold. My theory is that Aquasport used the small blocks simply as a way of using up scrap plywood. No one here, to the best of my knowledge, has rebuilt a deck using 6" x 6" blocks since they would yield an inherently weaker finished product. Anyway, as you do your reading, you'll learn all about the best way to tackle the job.
Please post pictures of your project and write up your progress as you go along. That's how most of us learn.