I cant tell you what traits are good or bad to cull out in whitetail, I work with fallow, red deer, rusa ,sambar & chital (axis). However the basic principles are still the same for deer ,cows, dogs, cats,etc.
Before we cross two different phenotypes we need to have a very clear objective in mind. I visualise that objective & write down & record exactly what I am trying to achieve. This is the "blueprint" I will cull towards. For some background, I also play around with the restoration of some sub species of deer. This means I have to undo hybridisation. For my Persian deer I look to places like the British Geographical Societies records & museum collections to get the clear picture of the phenotype or "blue print" which I am breeding back too, I cull to this. This also includes ecological traits such as the timing of the rut/fawning, I try to restore temperament or undo the domestication/taming that occurs even in zoos, as well as the phenotype.
It's going to be many years before we establish our new line (even with JIVET embryos, we still need to look at conformation not just pedigree). Place copies of your "blueprint" & objectives clearly in several places, near the crush, on the fridge, in the feed room, etc. This is to keep you focused, particularly with the F2 generation ,that is an emotional desert after the F1 generation. You must maintain the desire ,determination & discipline. It you doubt you can see it to the finish then stop at the F1 & make them all terminal.
I could bang on about producing several "identical" lines with several hundred animals in each generation carefully culled & selected. I don't think this is likely to happen & if it was, a forum is propably not the best place to discuss it anyway. What I'm guessing is practical is small herds of 50 or so deer in small private projects. If we have culled all our F1 & F2 animals along the way hopefully we have 50 F3 animals to select from (lots more would be nice). I would then pick the one buck that best conforms & several of the does which best conform to the phenotype we are seeking. I'd use him over all the does & tag & match up the offspring. I'd do this for a few years untill I could see which doe is giving us bucks which are the closest to the phenotype before trying to produce too many F5 (it'doesnt matter too much as you can always go back & do a big cull, but there are other opportunity costs involved like feed & space). Once I had established which of the does were dropping the best fawns, I would promote her daughters & they would be the dams of the F5 generation. The best F4 buck from this generation is used as the sire.