Dan,
The things that you mentioned vary between commercial boats also. There are general differences between Greenland, British, and Pacific Northwest designs for example. Most Current Design boats will have more deck height than say a Northwest Design or a Necky or Valley designs. Foot height is an easy one just sit against the wall and measure out to your feet. Now do the same thing in kayak foundry from about 3 inches in front of the back of the cockpit measure the same distance forward and measure the height and width of the cross section and compare to your foot height and width in paddling form. For deck height I suggest you sit in a few friends kayaks and find what you like and measure the front and back cockpit height as well as the cockpit dimensions. It really doesn't matter if you are buying or building it is good to pay attention to those details, understand why they are different, understand your own style and the nature of the water you are paddling in. The boat you designed based on your body size is a good general purpose boat, not a sports car and not a truck, it is in the Volvo league. I would ask for more comments on the blue heron site and be specific about how you plan to use it.
Scott