Recovering Chicken Abuser

Hey everyone, I recently cleaned out my chickens nest box and was disgusted by the smell and look. We got our Chickens a year or two ago and my parents didnt know much about chickens to give them a proper chicken pen, we put a 2x4 up for them to roost but its the same height as their nesting box so now they nest and roost in the box. This means that they’re accumulating waste in the box continuously getting it really nasty.

I plan on tearing down the box and rebuilding it to be much lower to the ground. The last image is a mock image to just help envision what Im thinking of doing. I plan on putting a dropping board over the nesting box under the roost. Is that image a much better idea for the pen?

In the meantime ive completely cleaned out their box, layered it with PDZ on the bottom for combatting ammonia, pine shavings, and then a hemp and herb blend and extra pdz on top to help remove insects, soak up liquid and keep it smelling fresh. When i stuck my head in there yesterday before cleaning it, it smelled horrible and i felt terrible about what i was subjecting my chickens to.

Im open to any orher ideas or suggestions. I recently got two ducklings and a gosling so would love to know any tips yall have for waterfowl. Thank you.