I refer to our 3 hens as pets with benefits. :) My daughters treat them like indoor dogs. Very spoiled, but they do live outside with our very vocal rooster boy.
I guess we got lucky with our EE roo too. Our birds were all 3 days old when we got them. We didn't plan for a rooster, but my kids became so attached that we still have him. He actually lets all of us pet him (even my huge husband) and will come when called by my teenager. He's never been...
I haven't bought eggs since October. I collect the eggs and rinse them off after a couple days. Then I use warm mineral oil to coat them. They stay on the counter. No one has gotten sick yet!
I enjoyed it tremendously. My husband did too, but he thought it was more like a mashing of original Star Wars and Empire Strikes Back. Still, Rey is an easy character to love.
I keep our eggs on the counter. After I collect them, I rub mineral oil over them, and the put them in cartons. I believe the US is one of the only countries that refrigerates eggs. Nobody has gotten sick yet.
http://www.preparednesspro.com/safely-preserving-eggs
You might want to post pictures. Also, if you have trees, I'm thinking your chickens have places to hide. I've heard others use avian netting. I myself have chicken wire and tarps over angled PVC framing. Still, if you post a picture, you might get a better response.
Our Chihuahua is fine with the chickens. Our beagle just stares. He's getting better, but we still don't let him get close. We're always out with him, and keep him on a lead when the girls are free ranging.
We wrapped our run in plastic too. Can't tell after the last two days of brutal winds. Frustrating. We just want our little buggers to be safe and happy, but Mother Nature isn't much of a help on certain days...