Ok so I had LOTS of problems solved up to the present moment. Need to get a little less perfectionist about posting. In brief:

• If you make your own PCBs, don't just trust the footprints for your components will work (both my rotary switches and my microswitches didn't have big enough drill holes: they had to be widened).
• Don't buy parts that don't come with a footprint diagram.

I have a new prototype which looks great:

It's also mostly intact on the back, including my shiny new PCBs! I have:

The shield (the thing that snaps on to the back of the arduino to provide connections to the other boards and analog devices)

The action panel (the thing that provides most of the digital i/o and which has the action buttons on it.

The throttle panel (which has the rotary switch inputs and some other i/o on it.

If I had known how PCB pricing works when I started, I would have tried to make one shield panel to go under the action panel and used surface mount parts. Maybe next time.

It is not, of course, working yet. At the moment I have a problem where, if I hook up a purchased i2c device (like the adafruit bar graphs) to my arduino with a breadboard, it works fine, but if I try to hook it up through my shield board, it doesn't work. So probably there is a flaw in the shield board (bummer). I don't really know how to figure out what it is though - guess I'll have to do some research :)