How does one avoid their chickens coming into contact with wild birds, short of keeping them locked in an entirely enclosed coop? Even if they're in a run, birds can and will roost on top of the run, pooping in it and dropping parasites if that's what your concern is. My birds free range, and as far as I know have never had a problem with parasites - internal or external.
OP, sounds like your chickens will do just fine. I truly believe that being able to roam keeps them healthier.(Well, except for potential predator problems, but as far as illness goes...) I don't know if you're planning on free ranging or not, or if you have a run attached to your coop, but here's what I do: When I move my chickens from one coop to another, or get new ones, I keep them locked in their run/coop area for about a week or so. That way they can recognize their new location as home. They will then return there to roost at night. If you don't have an attached run, but your coop is large enough to keep them in for a week, that's what I would suggest.
where the issue typically is with free range, is when they come in contact with bird's nests on the ground. in this area for instance, killdeer nest on the ground. if they have fowl mites especially, they will infest the nest and surrounding areas. and yes, internal parasites can be spread by manure, especially coccidiosis. nearly every North American flock has some sort of parasite, it is actually better for a chicken to have a mild case of worms than to be worm free. a few worms encourage eating and drinking bringing more nutrients into the body. most people will also experience either lice or mites or even both in their first year.
we are getting into an area here where i dont practice what i preach LOL, i encourage everyone else to make sure they get grass, bugs and sunlight. chickens who get out in the run get these things and are typically healthy, even with some illness. they can recover from most poultry diseases, and thrive again. the issue with this, is they become carriers of certain diseases. you then in some cases have to vaccinate any new chickens coming to your flock to keep them from getting a "carried" illness. Coryza, and mericks are a couple of these diseases. i myself am a little more commercial in nature, i cannot risk sending potential carriers out of my flock. we have around 550 chickens, penned in small groups - the largest being about 16 in one pen. if any of these pens show signs of illness, typically the whole pen is quarantined until the problem is known. sometimes nearby pens are also quarantined for safety reasons. if the illness is something that i could inadvertently send to a customer, the birds are culled - along with eggs in the incubator and potentially infected chicks. any "nearby" pens are watched for signs of the illness, and culled if needed. we maintain 2 separate flocks in separate buildings, in case one whole building had to be culled. a simple illness can cost me thousands, so i do what i can to prevent them. i am far from organic, but i offer organic solutions whenever possible, isn't that why most of us got into chickens? so we knew what went into what we were eating.
i am not saying the OP's birds have something - its just an issue that happens more commonly that most people realize. they asked what to expect with moving chickens and appear to be new at it since they just built a coop. im just telling them some of the things to watch for, and that there is a slim chance for some exposure.
to the OP:
don't let this discourage you from keeping chickens in any way! it's is an awesome hobby, most people become truly affectionate to their flock. more chickens are killed by kindness than disease. remember; chickens have no friends in nature, including themselves- so be prepared to the best of your ability. when you get stuck, there's almost always someone on BYC that can help you.
edited for spelling