My aft deck is 17.25" above the longerons, with the canopy continuing to rise to the same 17.5" dimension that I scaled from the KR2S drawing included with the plans. So mine is a "stock" KR2S from that respect. I'm right at 6 feet tall, my seat is about 1.5" from the bottom of the plane, and my headset will almost touch the Dragonfly canopy while flying, even without a cushion. Dan's advice to set up the seat AT THE FLOOR is excellent, and then adjust the canopy height to give you two inches or so of clearance. I will have to make a new seat shortly after flying, so I don't bounce off the canopy in choppy skies. The Dragonfly canopy's shape is very similar to that of the stock KR2S (see http://home.hiwaay.net/~langford/kcf.html for more details on that).
Definitely do the canopy first, and then the aft deck. You need the canopy in place when you build the aft deck, unless you like discontinuous flow lines and the disconcerting look that comes along with it, not to mention drag... Mark Langford, Huntsville, AL N56ML "at" hiwaay.net see KR2S project at http://home.hiwaay.net/~langford