I was just looking at your run again, I hope your going to have a way to lock up that top. Even a heavy piece of wood can be pushed out of the way if something wanted in bad enough.
It's big enough for him to sleep in for sure, but hopefully he won't be spending most of his time in there, I think e would be one very sad duck if he had to. Like others said if you plan on leaving him out over night, you better put something across the bottom for security . Way to many preds...