Whoa, very nice, man! You sound very thrilled to see that system working... and a bit panicked to hear the wife's voice :D

I do see room for improvement, as do you as well. The water that comes in the hugel - I'd channel that to go to the top swale or the middle one, or even the bottom one. A simple shallow and wide ditch would do, no need to dig a big depression. Not that the hugel won't absorb water, but currently it's very coarse structure as it hasn't decomposed much.

The top swale should certainly overflow down, etc. If you see too much of an overflow at the lowest part of the system, think about making the swales a bit wider at the top, I think you have the space. The top part is where most of the volume is as it widens.

How does the coop get flooded? Have you dug a drainage ditch on the higher sides of it? Have you tried simple french drainage? Where does the drainage lead? I think you should really get to work on that property map we were talking about :)