So they were laying before but are not now. That is interesting information. Are they molting? The best way to tell they are molting might be if you see extra feathers flying around. Are their combs and wattles bright red or sort of pink? Bright red generally means they are laying and eggs need to be fertilized. Pink means they are probably not laying and are not as sexually attractive.
Do they look that different from the other hens? Different colors/patterns? Silkie feathers or strange headdresses? Is he trying to mate with them? Where do they sleep, with the flock or separately? Are you north of the equator so it is fall?
I don't know if any of that has anything to do with his actions. Since he freaks out when you handle them he accepts them as part of the flock, he just doesn't want them to join the others. To me that sounds like strange behavior. Usually that would be the hens, not the rooster.
Since the two new ones were previously laying they are mature enough to join the flock. Often a lack of maturity causes problems but if they were laying they should be mature enough. Still, they will sometimes form sub-flocks and hang separately even when mature but with a sub-flock he should not be running them off food or keeping them away. That's what has really got me confused, him running them off of food. Are you sure they were laying before? Some of this behavior sounds like they could be immature pullets.
My first reaction is that as long as no one is getting physically hurt let it go and let them work it out. Integration can be stressful, there should be no long term effects of one of them being stressed out some now. Provide widely separated food and water stations to reduce competition.
My second thought is to lock the rooster up for a few days. See how the old and new hens react. If they merge into one flock he will probably accept them all when you release him.
I'm kind of stumped, some things just don't sound right. My standard approach is to let them work it out with as little interference from me as i can mange unless one is getting hurt. Good luck!
Ok so the two new hens, I believe are a bantam type brown Leghorn(she has a big red comb) and a small game hen. They are both older than my flock by at least a year, my flock is about 7 months old.
Originally I had them in a separate coop right next to the main coop for a month. I did not let them free range, but I let the othera out as normal and they were able to be around the coop and see the other two girls. After a month I let them free range together, are which point I let them all go into the same coop together.
Side note, they were from my father in law, so they stopped laying at first because of the move, made sense, but the Leghorn still laid once or twice a week, I witnessed it so I know it was her, but the game hen has never laid to my knowledge since we got her.
It does look like ahw is molting possibly, defintely more feathers in the coop.
Another thing is that the Leghorn doesn't put up with any bullying, she protects the game hen if anyone is mean to her, she also seems to have no problem getting food. The game hen is the one always hiding out alone away from the flock when my rooster isn't pushing her out.
I live in northern Nevada, the temps just started dropping to the 30s at night.
Hopefully this helps! I'll grab pics if I can.