Thanks for the photos. Here's my suggestions on how to convert a prefab/prefab style coop & mini run into a bigger coop, which should help fix space and ventilation issues:
So to turn it from 2 small "boxes" (tiny coop above tiny run) into 1 bigger "box" you'll want to remove as much of the inside coop wall as possible, plus the floor. Take out the old roosts too.
Nests might be able to stay as is, or may need to be relocated elsewhere or replaced - depends on the structure of the coop and how things inside stack up once done.
Run a new roost(s) lengthwise across the newly open space. Ideally you’d like 12” per bird but 10” can suffice in many cases.
Board up some of the external wire walls so that the roost area is protected from winds and rain. Do NOT fully cover up all the wire, you need ventilation and natural light, so at the very least a few inches under the roofline should remain open. If your climate allows for it, you can leave entire walls open with just the mesh, but I don't know how cold it gets in winter - though you also make it convertible for the season by covering up open walls for winter, and then uncovering for hot and humid summers.