I'd scoop out as much hay as possible into a bucket, then vacuum out whatever's left and the area where the bucket was. Make sure you dump the hay and vacuum where you ducks don't go, or in the trash. My ducks love piles of hay, and will pick through them for hours!
My ducks don't like bananas but I've read it was ok for them. I'm not sure what predators you have, but here it seems Pekins are large enough that hawks wont bother them. Mine also have trees to hide under, which they do sometimes.
The fencing around the ark, its cute but a loose dog could make a snack out of them fast.
I might have missed this, it once they go inside, make sure you give treats. You want them to associate their ark with treats, safety and comfort.
Thanks for taking these duckies on. I know you...