ChickenDanz, I'm sorry to hear about your roo. I've never seen anything like that, thank goodness.
Hawkeye, with any flock, there are bound to be a few losses. In our first few months, we lost two out of nine chickens and never did find out what it was. My best guess at this point is that it was something genetic or already past the contagious stage by the time we added those chickens to the rest of the flock (the third chicken of that batch is fine). Please don't let that discourage you from raising chickens. They are beautiful, curious creatures who are a lot of fun.
I'm envying you your coop building. We retrofitted my niece's old playhouse. It's adorable, works just fine, and was quite inexpensive. However, there are many things we'd do differently if we were building from scratch. I'm impressed with what you're doing and it's going to be a great home for your chickens.