Goodness you all have been busy today! It warms my heart to come home and see 19 posts to this thread! Colorado Chickeners rock
Aaron, welcome! As others have mentioned, you will find a wealth of information here and plenty of fellow chickeners in various stages of learning - not one of us thinks we're done. My comments on your proposed setup are that 9 square feet is enough for two, could be tight but do-able for three if you let them out to free range in your yard when you are home. I would not line the bottom of your run - I had originally intended to do so this time around, but opted against because it negates the benefit of foraging - the wire crushes the greenery underneath. If you worry about predators, you might try a few turns of polywire electric fence and a small charger (~$50 plus an extension cord rated for outdoor use). You also, I'm sure, realize that nothing is foolproof, and there will always be the chance of predation, illness, or general unthriftyness claiming a chicken's life. For the most part, though, they are pretty darned savvy critters, and when loose know how to find cover if it's available. For litter, I agree with Mountain Momma, deep litter works well, despite the seeming illogic of it. I saw an ad recently, here on BYC, posted by someone in CO who raises and sells RIR in CO, think they are in the mountains and pickup only, I know nothing about them but may be worth a call/visit. I would also accept the invitation of those who have offered the opportunity to visit and see how they manage their chickens - not everything will work for you but lots of ideas. And opportunity to meet some chickens and terrific chicken keepers!
Mice - might try the block type poison inside a piece of pvc so chickens can't get it. Or a cat. Indigenous control is largely absent this time of year (snakes) although birds of prey will provide some assistance, as will smaller mammal predators such as fox, but we don't generally want them around the chickens, so poisoning the mice will go some distance to keep them away from the perimeter.
Owls/Hawks/Falcons (nice pics, Rock Home Isle!) - someone on the OTs thread mentioned using a pole with fishing line strung off it like a maypole to keep flighted predators away and several who have tried it say it seems to have worked. For Bobcats ... big dog, or hooved LG like burros, llamas maybe? Or electric fence.
Wendell - nice job on your cages! I'm exhausted just reading what you got done today!