chicken canoe-----welcome aboard,
First I would try too get the incubated chicks used to me handling them from time to time.Its hard dealing with wild birds, i have a few myself.I have a hen that i have only touched 1 time in a year.I rescued her last year,my father-in-law was about to shoot her. He had a air conditioning case sitting out on the ground in the yard,and this wild speckkled sussex hen went broody and made a nest inside the case.Everytime my father-in-law would try to move the case the hen attacked him.I ended up catching her nest and all with a net........at night. Til this day I still cant touch that bird.I took her eggs and incubated them the rest of the way and raised them and they are now more friendly and i can touch them.And then some of those showed wild qualities as well.I know cock fighters that like to keep the wild factor in their bird's bloodline,on the the other hand many people like myself like a more user/owner friendly type of bird. So this is something i consider when culling.This wild hen i got is up for culling but her beauty keeps me from dropping the axe.....lol.......she is eye candy for sure.
I would also run several distinct lines of that breed, lets say 2.......Keep those 2 lines seperate over generations father/daughter or grandaughter ......mother/son or grandson.You actually have 4 lines going 2 male lines and 2 female lines. From my understanding you can basicly breed this way for years.when one flock loses vigor you can basicly bring in new blood from one of the other lines and rejuvinate the flock, I think it is called spiral breeding,where you keep your lines seperate and breed cousins for bringing vitality back to the breed. instead of the traditional line breeding.
Get those trapnests up and running and you set to go,sounds like a nice project you got going on.