Make the Chipotle Puree and get started on the Fire Roasted Salsa First (see directions below)
Rinse quinoa three times in cold water to remove the outer coating and drain.
Bring the water to a boil in a small pot; add a pinch of salt and the quinoa. Cover, lower the heat, and cook over low heat about 15 minutes, until tender. Set aside to cool.
Grill the chilies directly over an open flame (you can do this if you have a gas stove), using metal tongs to turn them until the skins are blistered and charred. Note: if you don't have a gas stove, you can roast the chiles in the oven (preheat your oven's broiler, and roast on both sides for about 10 minutes each until they are charred and black)
Transfer to a bowl, and cover; the chilies will steam as they cool. Peel the chilies, carefully removing the skin around the stems as you go. Make a lengthwise slit in each chili and remove the seeds. Set aside.
Preheat the oven to 375º F.
Heat the olive oil in a sauté pan and add the onions and a pinch of salt. Sauté over medium heat until the onions begin to soften, about 3 minutes. Add the corn, jalapeños, and ¼ cup water to keep the corn mixture from sticking to the pan. Cook over low heat until the corn is tender, about 5 minutes. Transfer to a bowl and set aside to cool.
Lightly oil a baking dish. Toss the quinoa with the corn mixture and season with the chipotle puree, herbs, pumpkin seeds, cheese, and ¼ teaspoon salt.
Stuff each chili with about 3/4 cup filling, depending on their size, being careful to keep the stems in place. The stuffed chilies should be firm, but not overly full.
Place them seam side up in the dish, cover and bake until the filling is heated through and the chilies are puffed, 25 to 30 minutes. Serve immediately.