Wash wheat berries well. Place in a bowl and fill with water. Cover loosely and let soak until wheat berries swell, 6 hours to overnight. Drain and rinse.
Divide wheat berries among 3 to 4 clean jars. Cover each with 2 layers of cheesecloth. Fasten with a rubber band. Rinse the wheat berries once a day with lukewarm water. Let soak in a dark, warm place, until grain is sprouted, about 3 days.
Preheat the oven to 350 degrees F (175 degrees C). Spread flax seeds, sesame seeds, and poppy seeds onto a baking sheet.
Toast in the preheated oven until seeds start to turn golden brown and become fragrant, about 4 minutes.
Reserve 1 cup sprouted wheat berries. Place remaining wheat berries, flax seeds, sesame seeds, poppy seeds, bread flour, whey, whole wheat flour, oil, maple syrup, molasses, gluten, yeast, and salt in a bread machine in the order listed by the manufacturer. Add the reserved 1 cup sprouted wheat berries when the machine beeps to alert you to add ingredients. Run Dough cycle, about 1 hour 45 minutes. Let rest for 30 minutes.
Preheat a pizza stone in the oven to 450 degrees F (230 degrees C).
Divide dough into 16 balls. Knead and shape into flattened circles and place on parchment paper. Cover and let rolls rise in a warm place until doubled into volume, 45 minutes to 1 hour.
Lift parchment paper to transfer rolls onto the preheated pizza stone. Reduce oven temperature to 400 degrees F (200 degrees C).
Bake in the preheated oven until tops are golden brown, 12 to 15 minutes.