Cut chiles in half lengthwise; remove stems and seeds. Set aside.
Combine water and quinoa in a medium saucepan; bring to a boil. Cover, reduce heat, and simmer 13 minutes or until liquid is absorbed. Set aside.
Spray a large nonstick skillet with cooking spray; place over medium-high heat until hot.
Add bell peppers, onion, jalapeo pepper, and garlic; saut 2 minutes.
Add pumpkin seed kernels; saute 2 minutes.
Remove from heat; stir in quinoa, green onions, cilantro, soy sauce, and lime juice. Spoon 1/3 cup quinoa mixture into each chile half.
Pour tomato juice into a 13 x 9-inch baking dish; place stuffed chiles in dish. Cover and bake at 350 for 20 minutes.
Sprinkle cheese over chiles; bake, uncovered, an additional 10 minutes or until cheese melts and chiles are thoroughly heated. Spoon tomato juice over chiles.