The problem with this question as I see it is the assumption that the flaws in humanity are genetic, not a matter of character. At least, in the form that they are perceived by the Christian God. This may actually be possible. In Genesis, God clearly tells Adam and Eve not to eat of the fruit of the tree of Knowledge of Good and Bad, then bars them access to the fruit of the tree of eternal life for doing so.
From that, we can infer that;
1) Mankind was made with in inherent flaw that caused them to age and die
2) If we'd been good for a set period of time, we'd have had that flaw reversed by some form of fruit containing a beneficial mutagen, that we'd have been given access to
So, from a philosophical perspective, we are genetically imperfect because of a character flaw that (after a given period of obedience) would have been corrected. Of course, this then brings forward the ultimate question;
Would correcting the character flaws to make us 'perfect' make us physically perfect according to biblical definitions (the wages of sin is death and all that)?
Religious perfection, particularly Christian religious perfection, is a matter of character, not genetics and cannot be otherwise. As such, it's not a selective breeding program you need; it's a selective training program. As such, there are plenty of fictional resources you can look to in order to understand such programs, but if we agree to stick with the classics for a moment, check out 1984 by George Orwell.
Humans are adaptable, curious, and loyal to causes that they believe deep down protect themselves and their interests. All you really have to do is give humans the right outlets for their curiosity (shape their environment), train them in the proper way to be (shape their adaptation to that environment) and then give them a suitable carrot (already built into Christian faith called Heaven) and you'd be amazed how quickly the 'perfect' human evolves.
It is important to note that the whole point of evolution developing the cerebral cortex was to allow intelligent animals, especially humans, to adapt to new situations within a single lifespan; not over millennia as the correct responses get encoded through trial and error into DNA. Your religious eugenics program is literally taking the most inefficient route to perfection possible.
You don't breed religious perfection; you inculcate it.