It sounds like your birds are both young & new? If that is the case they are still learning. Time & Patience are your friends.
Firstly your rooster is doing his rooster thing. Part of his job is to warn his girls of any perceived threat. You are a perceived threat. You are big & you are tid~biting his girls away from him when you offer treats. I have an all hen flock so I don't know much about roosters but unless he is submissive to you he is likely to become a problem when his hormones really kick in. Others here know heaps more about rooster behaviour.
As for your girls...set aside some large chunks of time ~ say 1/2 an hour. Put a low chair or stool in the run & sit quietly just watching them & letting them get used to you. Then quietly offer a treat ~ something irresistible like mealworms. I began by calling them:
tuk~tuk~tuk but people use whistles or bells, anything really that they can associate with good things coming their way. Scatter the treat but gradually drop it closer & closer to where you are so they get used to you. Remember, no sudden movements or loud noises.
The trust won't happen the first time, or the 2nd time, not even the first week, but over time, if you are consistent, your birds will learn you bring good things & will stop being so flighty. Some birds are naturally more trusting than others.
I have Campines, notoriously flighty & difficult. Don't like being handled. It took 10 months but this is Tuppence enjoying a cuddle. She is even relaxed enough to close her eyes & doze.
Hope that is helpful.