if I want to breed pure Ayem Cemanis...I have to keep them apart from other birds, correct ?
Yes, for the right amount of time. This may help with your planning.
It takes about 25 hours for an egg to go through the hen's internal egg making factory. The egg can only be fertilized during the first few minutes of that journey. That means if a mating takes place on a Thursday then Thursday's egg is not fertile. Can't be. Friday's egg might or might not be, depends on the timing. I don't count on it. Saturday's egg will be fertile.
A rooster does not mate with every hen in his flock every day, but he doesn't have to. In the final part of the mating act the rooster hops off, his part is done. The hen stands up fluffs up, and shakes. This fluffy shake gets the sperm in a special container near where the egg starts its internal journey. That sperm can remain viable from 9 days to over 3 weeks. So if you want to be pretty sure the old rooster s not the father you need to wait 3 weeks since her last mating with him. If you want to be very sure, wait 4 weeks.
Can this rooster be the one or should I assume he may be "related" and can't be the one?
Where did you get them? How big was the flock that was laying the eggs they hatched from? Most hatcheries have flocks big enough that you don't need to even think of that. Even with a small backyard flock it's usually not a problem. Chicken regularly interbreed or several generations before it becomes a problem, just don't use defective chickens as your breeders.
How exactly do I find out if they are fertilized and will hatch ?
Incubate them. If they are fertile they will develop. If you crack some and most have the bull' eye you can assume that the ones you don't crack also have it. This thread tells you what to look for.
http://www.backyardchickens.com/t/16008/how-to-tell-a-fertile-vs-infertile-egg-pictures
I do not know of any practical way to determine if an egg is fertile without either opening it or incubating it.
Will my hens just know to sit if I leave the eggs
It doesn't work that way. Many hens never go broody so no matter how many eggs pile up they will never go broody. They certainly don't go broody just because you want them to. The only way you can control when they hatch is to get an incubator.
WHEN do I suppose the rooster and hens will be able to create fertile eggs.
Pretty much when they start laying. It is considered best to not incubate the first eggs they lay. Sometimes they will hatch but hatch rates are often not very good with those small pullet eggs.
Can I leave the rooster with the hens as he has been since a chick ? Will he hurt them too young ?
No, lots of us do that. It can get pretty rough and people often freak out when they see that but to me that's part of them being chickens. The males do not have a penis that penetrates the females, sperm is transferred when they touch vents. The rough part is that the boys usually want to mate earlier than the girls do so the boys force them.
If I have the rooster in a mixed flock, I can assume cross bred chicks I suppose...so keep him separate or with just the AC if all I want are AC.
Unless you can tell which eggs are from the AC and only incubate them.
I have a Whiting blue I also wanted to breed, so this breed will need it's own coop as well
Yes
I will have to inject for vaccine..this sounds scary..is it easy?
I don't vaccinate mine so op experience with that.