Based on more analysis and brainstorming, I came to like the look and efficiency of a design by HyBrid Seattle, their c640h model.   Besides being attractive and livable, it would save a lot of time and solve the engineering challenges for us.  My contractor talked to them today and was encouraged by their willingness to work on it, without treating it like a complete prefab.  The idea would be for them to prep the containers and ship them to the site, and we'd be ready to drop them on a foundation with plans to finish the build.

We're sending them some more details on the site and goals, and we'll go from there.  The roof and upper story will be part of the discussion next.  It shouldn't be long before I have a cost estimate, now that we've removed a lot of the unknown factors.  I'm expecting to do some more permit research, but it looks like this will get us most of the way toward breaking ground.