In a a very large, glass,* microwave safe bowl, cook the eggnog and 1/2 cup of the milk until it just begins to boil, about 5-10 minutes on high.
While you boil the milk, in a separate medium bowl, whisk together the waffle batter, whole wheat pastry flour, granulated sugar, nutmeg and the remaining 1/2 cup of milk. Make sure you whisk the flour in slowly to avoid lumps.
Once the milk is just about to boil, quickly whisk in the waffle batter and continue microwaving, stirring every few minutes until the sauce just begins to boil. It does not need to boil a long time, you want to stop cooking it when it just starts to boil, this will take at least 15 minutes in a microwave.
This is what I did: My milk took 10 minutes to boil. Then I added the batter mixture and cooked 5 minutes, then stirred. Then another 5 mins, then stirred. I repeated this process once more for a total of 25 minutes, including cooking the plain milk. **
Take the cream sauce out of the microwave, and let stand to thicken while you cook the waffles, being sure to stir every few minutes so that the top does not develop a skin over top.