Okay, here's what I can do.
Wheat Changes: I can make it so that wheat plants don't drop seeds, and instead only drop wheat. I can also add flour and the ability to get seeds from wheat stalks. I could also probably make it so that you need to use flour to make bread, cakes, etc... But that would require more base class edits than I am willing to make right now. It would also make the chances of incompatibility with other mods higher.
Egg Changes: Making eggs cookable should be easy. It is just a matter of adding a nee item and a new smelting recipe.
Chicken Breeding Changes: Changing the way mob breeding works would be difficult. For now, I'll leave in the vanilla system, but add the incubator block, which allows you to hatch eggs into chickens with 100% of success. Eventually I'll change the vanilla mechanics, but for now I'll leave them in.
Cow Changes: This should be relatively simple, although it requires base class edits.
Sheep Changes: This should also be simple, although it also requires base class edits.