Exellent post!!! I am slightly worried about integrating my flock when the time comes and am at this time letting them see each other as much as they choose to without the babies getting hurt, when they are bigger I will put them out with the others and will watch for overly aggressive behaviour, I understand the pecking order and never have stopped the normal "I'm boss, clear out" behaviour. The older flock is non hatchery stock but although the 19 babies are incubated chicks they are the offsprings of the hens and Roo... I do worry about them never being accepted.Have hope and keep trying.
In my experience, this is normal behavior for artificially bred, reared and housed chickens, or the offspring from those that descend from such a recent ancestral environment and social structure.
They've lost the instinct for the natural family group after being reared without mothers, fathers, and a normal varying-age group flock structure for many generations. The instincts will come back if you let them, though it may well take generations. But you'd need to breed them naturally, and separate or not breed those which show absolute intolerance and violence to others. Some of your current flock may never adjust to other birds, as they often can't outgrow the faulty instincts in one generation.
Getting birds from a hatchery often means you get birds which are only tolerant of their own age group, gender, and type. Birds from any breeder who separates flocks and artificially rears them are rather often behaviorally/instinctively confused and aggressive to others.
This isn't a problem I ever have with my non-hatchery stock. Injured or ill birds are not harassed, babies range unmolested with mothers among the whole flock, roosters get along without fights, it's all very peaceful. It IS possible. But I remove or rehome bullies and violent birds, and won't breed any that show negative mentalities. So if you're not keen on doing that, then you may just have to work around your resident bullies/killers indefinitely.
I'm not saying my way is the only way, but it's best for me; what's best for you may be different. I need my flock to freerange in peace for health and productivity's sake, I won't keep birds that harm others or won't get along. Genetics have a lot to do with this, but so does environment and rearing.
Both genders can get along with others of all breeds and ages. All you need to do is remove any that absolutely will not tolerate others, or at least don't breed them, and breed those that do. In a few generations your flock will regain instinct.
Best wishes.
Also, The three month old boys were rasied with the flock and since realizing they were in fact males and not the hens I was hoping for I figured those two would have to be culled, but after spending all day outside working my husband and I both remarked that the youngsters spend 75% of their time with the Rooster, he tolerates them just fine and even still finds food for them. we figure they are learning how to be a Rooster, of course neither of them have started trying to crow yet so time will tell if he is still accepting of them then.