Haven't read the whole thread yet, but the first thing is to get good type. The saying is "build the barn first, then paint it."
Unwanted recessive traits are easier to get "rid" of by breeding in the dominant trait. However, they can continue to pop up for many generations, especially if the gene pool for the variety is small. Dominant traits are more difficult to get rid of, but once they are gone, they are gone.
In my opinion, first you want body type. All else comes after that. If you cannot afford excellent stock to begin with, find birds who have great type, but have DQs or faults that lower their $ cost. Try to get birds that complement each other. If one has poor or missing toes, the other should have good to excellent toes. If one is lacking crest, the other should have an abundant crest. Etc.
Expect that it will take years to breed poorer quality birds into good ones, and the cost to raise babies until you can determine whether they will be an asset or detriment to your project can make it as, or more expensive than purchasing good birds to start with, although the expense is spread out over a larger timeframe.