I'm finally building a coop! Advice please

Hi all. I currently house my chickens and ducks in a 12X12, well ventilated, predator proof, box stall. Every morning I let them all out to free range. I am happy with this set up, and I am spoiled. I love to be able to walk into the "coop" to clean and feed. Unfortunately, I need the stall back for horses.

I have decided to build a run, and a chicken coop in the run. Sometimes when we leave the ranch for a few days (rare, lol), people who come in to feed the critters can't get the chickens in at night. This way, caretakers won't have to worry about finding chickens. I still plan to free range.

Right now, I have 4 laying hens and a rooster. A Mallard drake, and two ducklings one I think, is a drake? 6 1/2 weeks old one is starting to quack, and the other just whistles. I also have 3 chicks that are 7 1/2 weeks old. Unfortunately, two of my "Pullets" will be roos. So, long term, hope to have 5 laying hens, a rooster, and a pair of ducks.

This is a picture of the beginnings of my run. It is 20X20, and six feet tall. The fence is welded pipe (thanks to my SO and his friend!).
Question number one. My boyfriend wants to use what I think of as garden fencing...green with 2"X3" rectangles. I think that this will be too large and that critters can get in. So, Is chicken wire strong enough, or should we go with steel netting? Or use the garden fencing and line it with chicken wire on the bottom?

Question: There are 2 cedar trees in the run. I am worried that if the chickens roost too high in them, that they will be able to fly out. Should I clip wings, or put a netting over the top?

I'm going to need space inside for ducks and chickens. Should the ducks just cruise around on the floor, or should I put nesting areas for them?
I am thinking that I want a floor, not just dirt in the coop itself. Right now, the stall they are in is a mat floor which is permeable so water soaks through, but floor stays dry...easy to clean.

At any rate, I am just beginning. I have learned a lot from this site! I know I will need ample ventilation, probably won't insulate (I live in high desert...90's summer, low teens winter. We (usually) have monsoons in summer, and several snow falls in winter. Our windy season is windy! Comes from all directions and can get up to 40 mi gusts.

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