I am not able to pull the tray out if I had any pine shavings on it. It just got stuck or everything skimmed off into the coop below. The shavings in the nest boxes stay pretty good now because of how I attached the brace for the roost poles. it added about three inches as a barrier between the box and the tray.
Wow, I wish i had such a large area to let them out into!! The coop's small run is just so tiny

We debated just creating a big secure run for them, but I decided I wanted to do a full rebuild due to the poopy eggs

No one likes poopy eggs! If you have bedding material on the tray then you might not get poop on the eggs like mine though. The poop would be mixed in with the bedding and not just glops of it piled up like in my coop. So you probably won't have to change anything now that you have nicer roosts.