I have a few thoughts and a recipe that may help you.
First, you might want to consider using the relatively new version of whole wheat flour sold by King Arthur. It is a white version of the traditional whole wheat flour but has the identical nutritional value. The particulars of the KA white whole wheat flour can be seen at http://www.kingarthurflour.com/shop/detail.jsp?select=C79&byCategory=C126&id=3311
. You might also want to take a look at the organic whole wheat flour sold by King Arthur, by clicking on the applicable photos at http://www.kingarthurflour.com/shop/list.jsp?pv=1192463284117&select=C79&byCategory=C274
Second, whole wheat flour hydrates (absorbs water) much more slowly than ordinary white flour. That is because the wheat germ and bran in the whole wheat flour just take longer to absorb the water. So, if the whole wheat dough seems sticky when you end up kneading it, don't panic and start adding more flour. If you do that, you will end up with a dry and stiff dough that will not give you the results you want. Just let the dough rest and slowly absorb the water.
Third, you don't have to go cold turkey in transitioning from white flour to whole wheat flour. You can do it in steps, starting with a mixture of white flour and whole wheat flour and gradually increasing the amount of whole wheat flour in relation to the white flour. You can also try using small amounts of other flours, like rye, for added flavor and nutrition. There's plenty enough protein and gluten in the whole wheat flour that you shouldn't have to add vital wheat gluten to compensate for the small amounts of gluten in flours like rye. You can also use soy flour for added nutrition, but only in very small amounts because it has a potent flavor in its own right.
Fourth, you might want to use honey as all or part of any sugar you use in your recipe. It nicely complements the earthy flavor of the whole wheat. I would use a robust and intensely flavorful honey, not the mild ones like red clover whose presence might end up being lost in the finished crust. The biggest challenge you will encounter using whole wheat flour is learning which cheeses and toppings to use. I would do a Google search to get ideas. I suspect that you will find some good ideas for white pizzas (non-tomato), as well as use of mushrooms and other earthy toppings.
I have posted a whole wheat dough recipe below that I saw Wolfgang Puck make on cable TV. I tried it once and thought it was quite good. The recipe calls for use of a food processor, but it can also be adapted for a stand mixer. Mixing by hand will be a lot tougher, so I would try to use a machine if at all possible. Good luck and let us know if you come up with some good ideas.Wolfgang Puck’s Whole-Wheat Flour Pizza Dough Recipe
For the dough:
1 packet active dry yeast
1/4 c. warm water (around 105-115 degrees F), plus 1 c. cool water
1 T. honey
3 3/4 c. whole-wheat flour (a mixture of 1 1/2 c. whole-wheat flour and 2 c. unbleached all-purpose flour may also be used)
1 T. olive oil
Dissolve the yeast in the warm water. Add the honey and let sit for 5 minutes, until the yeast-honey mixture is foamy. Put the whole-wheat flour in a food processor. Mix the 1 cup of cool water with the olive oil and salt. With the motor running, pour the olive oil mixture and the yeast mixture slowly through the feed tube. Process until the dough forms a ball on the blade. Transfer the dough to an oiled bowl, turn to coat, cover, and let rise until double in bulk. Punch down the dough and knead it on a lightly floured surface for 1 minute. Divide the dough into 4 equal portions and roll them into tight balls. Place on a tray, cover with a damp towel, and let rest for several hours or overnight in the refrigerator.
When ready to prepare the dough, roll or stretch each ball of dough into a 7-inch to 8-inch circle. Place the circles, one at a time, on a wooden peel or on a baking sheet and build and bake the pizzas (preferably on a pizza stone that has been preheated for one hour at 500-550 degrees F).