Once I knew the difference in grinding my own grains vs just whole wheat flour the answer was simple.  I need to buy grain and mill.  Whole grain literally has the entire grain ground into flour.  This is healthier for you heart, contains fiber and is rich in nutrients.  In regular all purpose flour the good stuff has all been pretty much removed.  The problem I have is trying to convert everyday recipes into whole grain ones.  I can tell you that it has not been easy.  I was bummed that there are not many good recipes available on the net and so I decided to go ahead an put mine in my blog.  I have not ran the numbers but overall it is cheaper to mill your own grain and we know it is healthier.
I altered a recipe I found in my baking book.  I would love to credit the author and I will try to email him but I do not need an cease and desist letter if you know what I mean.
I wanted a real tasting pizza dough, not something gummy or heavy.  I found this to be PERFECT.  I did use all purpose flour but with using almost half the amount of flour as whole grain I think it adds something back to what is normally not a healthy food in the first place.


2 cups hard white wheat flour (freshly ground)
2 1/2 cups all purpose flour
1.5 teaspoon instant yeast.. ( I added more because I made a quadruple batch and when you freeze dough you lose some of the yeast.
1 3/4 salt (never skimp on salt in bread recipes, it is there to help control the yeast and adds flavor)
1/4 olive oil
1 3/4 cups water ice cold
semolina flour or cornmeal for dusting.. (I used cornmeal)

Stir together flour, salt and instant yeast in a large mixing bowl.  (electric mixer preferred) stir ingredients and add the cold water and olive oil.  Mix on low speed with paddle attachment until blended.  switch to a dough hook and proceed for 5-7 minutes.  Dough should be clearing the sides of the bowl but sticky enough to stick to the bottom of the bowl adjust with flour or cold water accordingly. 
Flour up your hands and transfer to counter.  Make into 8 oz balls (I weighed mine) each 8 oz will make a 12 inch pizza.  I took a gallon zip lock and poured some olive oil in it and placed 2 balls in each one.  I froze some of mine because I had so much.  I placed 4 balls into the fridge and let it sit for 24 hours.  I waited 48.  Take dough out 2 hours prior to cooking.  Pat each ball with flour and olive oil into  1/2 inch thick 5 inch patty.  Cover with wrap.  Get oven as hot as you can 500 is good higher is better.  Using your hands stretch into pizzas.  If dough is not stretching let it rest for a few minutes and try again.  Use well floured hands.  I used a cookie sheet with corn meal to slide pizza off, place dough on sheet and add toppings.  Caution-- pizza with more then 3 toppings does not cook as well.  You want to cook your pizza fast 5-8 minutes.    Here are some pics of mine.  I would resist the urge to use a rolling pin and learn to stretch the dough with your hands.