Sounds to me like you're doing it right. If I lived near you, I'd buy EEs from you!
I think YOU'RE becoming the breeder that you're looking for.
As far as separating your hens, you're right. Separate for 2-3 weeks before introducing your favored roo. Doesn't matter if you remove the roos or separate the hens.
Also, three things come to mind for your EE problem.
First, where in the world are you? I just hatched a batch of blue and black Ameraucanas simply to get the roosters I wanted for my breeding program. I have six, and will be selling at least four. If you're close, or you are coming to the Ohio National Poultry Show (it's in my backyard, practically) I will sell you one cheap.
Secondly, do you ever get any broody hens? I've found that I get really great hatches from shipped eggs under a broody hen. You can talk to Ameraucana breeders on the Ameraucana thread here on BYC, and many will be willing to ship you out some eggs quickly after a lady goes broody for you. I paid $35/dozen including shipping, which was a good price. Then, you have your reliable source of blue egg genetics and you can take it from there.
Finally, you can search out an Ameraucana breeder near you. One of the best ways to identify a "real" Ameraucana breeder is if they tell you the color of the birds up front. In other words, "Americana chickens lay blue and green eggs" are likely to be Easter Eggers. "Wheaten Ameraucanas" are much more likely to be purebred. Then, ask the breeder what lines he/she used in their breeding program. They should know, and if they mention a feed store or a hatchery you'll know they really have EEs.
If you can get actual Ameraucana roosters, it simplifies your breeding program immensely because anything you breed to them will throw a green or blue egg.