I can give that a try. I do have a small roost on the one end of the run, seen in the first photo I posted, opposite the little jungle gym. Would that be an issue if they are up there and fly down from that? With the jungle gym in the middle of the run, it would be in the way of them jumping down from that. I can always remove that, or change the position of the roost to connect to the tower.
Shouldn't be an issue with the roosts in the corner, however it's hard to tell until they try using it with the gym in the way. You may need to make tweaks with positioning of things - I'm constantly moving things around the run to account for weather, potholes the chickens have dug, etc.
And yes the feather explosion sounds like a lighter all over molt, especially with the pin feathers and the "feathers flying off when they flap." So that might them behave a little off, as they're crankier than usual.