Great question. Yes, you can mill your own whole wheat flour! Note that the protein content in whole wheat berries and gluten quality can be highly variable. The whole grain flour we supply is typically a Hard Red Winter Wheat, but you can use your white winter wheat in a 1:1 substitution.
I do not recommend substituting your freshly milled wheat for the high extraction flour. It is much more challenging to approximate the T85, high extraction flour.
What kind of mill are you using. I love my Mockmill.
Hope that helps.