My coop is almost done and it's 140 sq. ft. on the inside and about the same for the outside as well. How many chickens should I start with? What breeds do you recommend for a newbie?
What are your goals for having chickens? Eggs, meat, pets, to show, because they are neat and do funny things, their fertilizer makes good compost material, you want to develop a new breed, you really like the weird looking ones, something else, or a combination of these? What you want to do with them makes a difference in what to recommend. How many eggs do you want? You need to do something with them and they add up in a hurry. Your climate does affect the choice in breed and number, mainly how cold it gets in the winter and how much snow you get. Does size of egg matter? Full sized or bantam makes a difference. As someone mentioned, the rule of thumb on this site is 4 square feet per chicken in the coop and 10 square feet per chicken in the run for full sized fowl. Neither is an absolute minimum especially if the other dimension is bigger but there are a lot of factors involved. I'd suggest instead of looking at how many chickens you can squeeze in there, you decide how many chickens you want then make sure you have enough space for them. Don't forget to leave space for baby chicks in the future.
I have heard that if I get a rooster he must be kept separate from the hens?
Why? Roosters have been living with hens for thousands of years. There would never be baby chicks if they were always kept apart. There can be legitimate reasons to keep hens and roosters apart, like a breeding program and you want to control which rooster mates with which hen, but I have trouble responding to that blanket statement. Without more information, I can't imagine why they must be separated.
I would like to have the very dark chocolate eggs, some light brown, the easter eggers-basically just a nice mix of colors would be great. I am sooo excited!!!
Marans and Welsummers can lay dark brown eggs. The hatchery chicks are not bred to lay the dark brown eggs so their eggs can be lighter than the really dark brown eggs some breeders go for. They should still be darker brown than the others. The Easter Eggers can lay either blue, green, or brown eggs. You never know for sure what you will get. With the other breeds, it varies some by breed and some by individual. Henderson's Breed Chart gives trends and tendencies by breed, but it can really vary by individual, especially with hatchery chicks. You can look at photos of the individual breeds at Feathersite.
The Henderson chart
http://www.ithaca.edu/staff/jhenderson/chooks/chooks.html
Feathersite
http://www.feathersite.com/Poultry/BRKPoultryPage.html
I would like to have a variety of hens and I was curious if the type of rooster would have an effect on the later generations. Like if I had a good egg layer and a rooster from a bad egg laying lineage fertilized one of her, would the baby be a mediocre egg layer?
There are a lot of different genes that influence egg laying. The rooster contributes some of those genes, so, yes, he will influence how well the offspring lay. Whether a particular offspring will be a good, mediocre, or bad layer just depends on how those genes happen to come together, but if egg production is one of your goals, I would strongly recommend a rooster from a breed that is known to be a good egg producer.
Good luck! You are off to a great adventure.