Bris,
Having built both styles of the Cirrus I can see no pressing need to re engineer it. Vaclav has an excellent design and sound construction methods plus excellent instructions. And he will answer questions. My Cirrus has bounced over rocks and generally been paddled like a normal kayak, no problems of any kind. A hint for the hull to deck join; put the glass tape on the inside hull with small dabs of hot melt glue prior to joining the halves. The tape just naturally flops into place when the kayak is put on edge and glassing it is a snap. Relax and enjoy, the construction is as much fun as the paddle!
Dave