You coop has a great design. The live edge siding is beautiful. I’m going to assume you put the plastic up to “insulate” the walls and avoid drafts. You shouldn’t need it since you overlapped the siding. I wouldn’t add siding over it, just take it out as much as possible, or they will shred it.
The windows over the roosts are high enough that frostbite shouldn’t be a concern, plus the ventilation around the roofline on the front and back should be plenty sufficient.
If you flip the laying boxes on their sides, definitely raise them a few inches to accommodate the DLM. Just make sure the top of the box is well below the roost height or they will end up sleeping on the box.
One 2x4 is plenty of room for them to sleep on. Remove the one closest to the wall.
You’ve done a good job. If you end up with problems, you can always go back and make modifications later. You will always find little tweeks you want to make.