Three chickens is probably best. The chicken is a very social bird, and they do well in groups. A pair could be a bit small without a lot of human interaction. Secondly, if you only plan on having two or three, you don't need a 5 x 3 coop. You could do 4 x 4 or 3 x 3. They'll fit in both. As for the run area, the number of birds that you gave would fit in there, but I generally like to give the birds as much room as possible in the run, about 10 sq ft per bird for mine. The number is flexible, but outdoor space is much more important than indoor space. As for roost bars, which they will use to sleep on, a 2 x 3 or 2 x 4 wiill do. Something that they can stand on without having to curl their toes too much works best, because in the winter they will lay on their feet to prevent frostbite. Nest boxes are usually in the realm of 12 x 12. One box will be enough for 2-3 birds. I wouldn't waste space on that. I also would not put the roost bar right on top of the next boxes or close to them. This could potentially cause the birds to sleep in the nesting box, and you will be out there cleaning a lot to prevent dirty eggs..
Lastly, I'm not sure what kind of birds you want, but with 2-3 birds you won't get a whole lot unless you have a production like breed. Sex links and production hens lay an egg a day. Heritage birds like Rhode Island Reds and Australorps are also very reliable layers. Other breeds that lay 3-4 eggs a week won't even give you a dozen a week.
