The conversion that 3KillerBs linked you is intended to illustrate how to convert a tiny coop-run combo, into a bigger coop-only build. As you already have a large run that tiny run space can easily be repurposed into coop space. Depending on your climate that can mean closing off some of the walls.for the first link you posted about someone renovating their prefab, i don’t understand why they used wood and covered up the sides of the coop? isn’t the free flowing air good?
I will post you the instructions I gave which led to the converted coop you saw:
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 or widthwise across the newly open space, depending on how much roost is needed. 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, or make it convertible for the season by covering up open walls for winter, and then uncovering for summer.
Example of a modified prefab: https://www.backyardchickens.com/threads/my-renovated-prefab-coop.1440258/
Netting is fine for the top as long as you realize that it's mostly effective against aerial predators, and not intended to keep ground based predators at bay (it can, but isn't nearly as secure as a roof, for example). So if you intend to stay with netting, it is important to keep the coop latched/locked up at night, when ground predators are more likely looking for an easy meal.i will look into wrapping hardware cloth on the run, and what do you suggest about the top of the run?