With all your broodies, they are going to be mating their sisters too. If you go through the genetics, that's no worse than son to mother or father to daughter as far as matching possible bad or good genes. With a mother or father involved, you just concentrate the genes from that side of the family. I'm not sure if any of this makes a rooster his own uncle, but it may make the offspring not only siblings but cousins. I think if a mother or father is involved instead of siblings, they are first cousins once removed as well as siblings, but I haven't had enough coffee to work that out yet. Or are the offspring their own aunt or uncle instead of cousins?
What you are proposing is not at all unusual. When you inbreed like that, you may be enhancing good traits or bad traits, maybe both. I can't tell you how often you need to bring on new blood. I just don't know. I do it every couple of generations, but there is still a lot of inbreeding going on. Other than the physical deformities you might see, too much inbreeding can cause a loss of fertility, loss of vitality, or decreased egg laying, things like that. If you can select your hatching eggs from hens that lay a lot and that have a pretty good proportion of their eggs hatch, you can keep going longer without bringing in new stock. That can get pretty hard to do with the way I think you are set up.
I think your plan is pretty good. The way I understand it, yours have two different coops but do have some overlap in grazing range. When you do hatch them out, I think you may find there is more going on behind the wood shed than you think. I'm trying to think what a naked neck brahma would look like.
Go Impy!!!!