I agree with prariechicken on security. It's what I would do if I could.
But please don't feel bad about telling us how you feel. Most of us on this forum have chickens as pets and they do become our children. We all have our favorites, our buddies, and, unfortunately, they seem to be the ones the preditors get first. I am very sorry for your loss. Could you perhaps hatch some of the fertile eggs from your hens? You can never replace your precious roo, but if you had some of his children you would have something to remember him by.
You're not crazy, Billy Bob was family, he just came wrapped in feathers......
Your run should have a chicken wire top, a chicken wire apron with rocks on top. Nothing can fly in, or climb in and nothing can dig under that way. I used 2 ft tall hardware cloth around the bottom perimeter of the run so little hands can't reach through to grab chickens while they sleep. With a few changes your new rooster will be very happy and safe. Again, so sorry to hear about Billy. Hugs! 
