Preheat oven to 450 to 475 F and fit the oven with a pizza stone. Bring the dough to room temperature and flour lightly to shape. Starting in the center, push the dough out from the center to make a circle.
Once you have the shape and thickness you desire (everyone has their own tastes) place the dough on a cutting board or pizza peel dusted with semolina flour. Brush the edge of the pizza dough with olive oil.
Dress the pizza with goat cheese and peppers. Slide pizza onto the stone in the oven and close the door. It is important that the pizza stone is hot to develop a nice crust. Depending on your oven, you may want to rotate the pizza on the stone to ensure even cooking.
Once the outer crust has achieved the desired color (once again, there are a few schools of thought here, some prefer deep brown crust, while others prefer a blonde chewy crust), remove pizza from the oven, garnish with generous amounts of crispy shallots and fresh thyme and eat right away.
Chef Dan McHugh's Note: The longer you wait to eat the pizza, the more you risk the crust becoming soggy. It usually depends on what you put the finishing product on: ceramic is the worst and wood is the best.
In a small bowl, dissolve the yeast and honey in 1/4 cup warm water.
In a food processor, combine the flour and the salt. Add the oil, the yeast mixture and the remaining 3/4 cup of water and process until the mixture forms a ball.
The pizza dough can also be made in a mixer fitted with a dough hook. Mix on low speed until the mixture comes cleanly away from the sides o the bowl and starts to climb up the dough hook.
Turn the dough out onto a clean work surface and knead by hand 2 or 3 minutes longer. The dough should be smooth and firm. Cover the dough with a clean, damp towel and let it rise in a cool spot for about 2 hours.
When ready, the dough will stretch as it is lightly pulled. Divide the dough into even balls and shape, let rest at least one hour before tossing. This dough will keep in the fridge for two days if it is tightly wrapped.
Slice shallots thin but not paper thin or they will burn. Spread them out in a single layer to dry out while the oil heats; this will result in a crisper shallot. Heat the oil in a heavy pot to 325 to 350 F.
Chef Dan McHugh's Note: He uses a Dutch oven and a thermometer, which helps him keep the oil temperature accurate.
Fry shallots in small batches until they turn from white to golden brown. Remove from the oil and salt immediately. Once the shallots cool completely, they'll become crisp. They will keep for at least 24 hours covered tightly at room temperature.