You will get many opinions of this subject - here's my $.02
The outside run fence should be at least 6 feet high. Covering the pen depends on where you are and what predators you have. I leave mine open on top and haven't had any problems, other than a chicken or two flying out to free range before I open the door to the bigger grazing pen (about 1/2 acre with my sheep). I do clip the wings in an attempt to keep some order!
Burry the wire about 6 inches down to deter digging animals and because chickens do a lot of scratching. I weight my wire with a trench of rocks and also bend it into the coop about 6 inches. The rats still find a way in, but its manageable.
The run itself is a dirt ground. In the spring and fall I add layers of mulched leaves, wood chips from any tree work we've had done, and grass clippings (not too much or it just gets spongy and smelly). I also turn the dirt now and then to bring up the worms as a treat. I dig down a few inches and use the dirt for my flower boxes in the spring, but be careful with this since chicken poo can burn plants easily if its not aged.
My coop is raised off the ground about 18 inches, made of very thick, sturdy wood (not pressure treated). This sucker was built in 1925 and is still going strong! I did put a fresh coat of paint on it 2 years ago. I have 3 windows for ventilation, closed in the winter, open with screens in the spring/summer.
The actual indoor coop doesn't have to be high (mine is about 4 feet), but keep in mind the cleaning. I WISH mine were high enough to stand up in - its a pain (literally) to muck out. I put all the shavings and poo on my garden in the fall so it can age over the winter and be ready for May planting. The rest of the year I make mulch piles to use later.
General guidelines are 2 sq ft minimum per chicken inside coop, 8 sq ft per chicken for the outside run. Overcrowding leads to disease, pecking, overly messy pen, etc.
Roosts 1-2 feet up is fine. Use rectangular wood (2x4s are good) so they can have their feet flat and sit on them to keep warm in cold weather. Rounded roosts leave toes exposed to frostbite, etc. You can also make a ladder system for them to roost as different heights. Just make sure there is plenty of room for all the chickens.
Nesting boxes should be up off the ground to encourage them to use the boxes rather than lay on the coop floor. I use straw in mine and have to clean them regularly since some chickens also sleep and mess in them. I tried pine shavings but they just kick it out. Not sure how many boxes you need - I have 6 for 18 hens and they mostly use 2-3 of the boxes.
I do use pine shavings on the floor of the coop - it makes the mucking out so much easier. Chicken poo is like glue!
Try googling "chicken coops" "chicken nesting box" "chicken roosts" "chicken pens" choosing Web and Images in the upper left. There is a ton of great info out there. Good luck!
