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ducking under a roost is not necessarily a problem. Probably the worst height would be like 10" or so (above the bedding), since that way it is neither easy for them to go under *or* over it, so I would suggest higher or lower than that.
what about moving the one that is very close to...
I am not quite getting why you can't manually put them on the roosts. If it is because you lack access, make a hinged panel that you can open TO put them on - someday you will need it for other purposes anyhow, such as catching an injured bird or doing *thorough* cleaning.
So I would suggest...