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I like the idea of using siding to match the house. I need better orientation--in the pics looking broadside at the coop/house, are we looking north, left is west and right is east? How I might proceed would be very much influenced by the coop's orientation.
My birds only use the elevated area as a way to get to the nest boxes and up to the roosts (and back down again), so no, it's not necessary at all. I think it does provide a better shelter in the winter as the bottom is entirely open on three sides. But really, it's not necessary.
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So, it's generally advisable that the door between the coop and run be closed at dusk and opened at dawn to limit predation. Having said that, my pop door is open 24/7. We travel a lot and I don't want the house sitter to have to deal with opening and closing it. By not closing the coop at night, I expose an extra 40' of linear space for predators to get in for a total of 54' of risk, compared to just 14' if I locked them up at night. I don't worry too much, because I think the run is about as predator proof as the coop. The increased risk I incur doesn't seem to offset the energy required to open and close it every day.
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I don't have poop boards but I think they are a good idea, especially for someone like me that is fairly fastidious about coop cleanliness. I figure that if it's easier to keep clean, you will be more likely to keep it clean. In my urban situation, that is a important goal. I don't know for sure, but I suspect your birds will appreciate a wider roost. Mine do catch some droppings, but I keep a 6" drywall knife in there that I use to scrape it off when I rake the floor. It adds less than a minute to clean up time. Maybe others with more experience will have other ideas. I'm not sure why chickens would drop from the ceiling---well now that I think of it mine have occasionally fallen off the roost when they are fighting over prime roosting areas right at dusk.
