I used whole wheat white flour (it's lighter in texture and naturally sweeter than regular whole wheat) and all natural PB. Husband couldn't tell these cookies were 100% whole grain and gobbled them right up. I chilled the dough for a few hours, and instead of forming balls, I just used a medium cookie scoop to get uniform-sized rounded mounds in the fraction of the time. I dropped the mounds into regular muffin tins because that's all I had, but they still came out looking great.
I did have to cook them 3 min longer though because I made them larger than what the recipe called for. Don't make the mistake of cooking them too long (recipe is right on unless you make your cookies bigger). The dough should be soft when you take it out. The first time I made this, I baked them too long (waited for them to turn golden), and they were dry.