Preheat the oven to 350 degrees F. Pat the short ribs dry and season all over with salt and pepper. Heat the canola oil in a large Dutch oven over medium-high heat. Working in batches, brown the short ribs on both sides, about 8 minutes total. Remove to a plate.
Meanwhile, combine the stock and dried chiles in a medium saucepan and bring to a simmer. Remove from the heat and let steep, 15 minutes.
Discard all but 3 tablespoons oil from the Dutch oven. Add the onion and cook, stirring, until soft, about 5 minutes; add the garlic and cook 1 minute. Pour in the red wine and port and simmer, stirring, until almost completely reduced, about 12 minutes. Add the thyme and chile-stock mixture; bring to a simmer and return the short ribs to the pot. Cover, transfer to the oven and cook until the meat is tender, about 2 hours, 30 minutes.
Remove the short ribs to a bowl; shred the meat from the bone. Strain the cooking liquid into a degreasing cup and pour off the excess fat. Pour the remaining liquid into a skillet and bring to a boil. Reduce to a simmer and cook, stirring occasionally, until thickened, 10 to 15 minutes; season with salt and pepper. Add the meat and toss to coat. Fill the taco shells with the meat; top with cilantro, Queso Sauce, Pickled Onions and Chile Relish.
Melt 1 tablespoon butter in a saucepan over medium-high heat. Whisk in 1 tablespoon flour; cook 1 minute. Slowly whisk in 1 1/4 cups warmed whole milk; cook, whisking, until thickened, about 5 minutes. Remove from the heat and stir in 3 cups grated Monterey jack and 1/4 cup grated parmesan; season with salt and pepper. Serve warm.
Pickled Red Onions:
Bring 3/4 cup lime juice, 1/4 cup each red wine vinegar and sugar, and 1 tablespoon salt to a boil in a saucepan. Remove from the heat and let cool, 5 minutes. Toss with 1 thinly sliced red onion in a bowl; cover and chill at least 4 hours, stirring occasionally.
Green Chile Relish:
Broil 2 poblano peppers until charred on all sides; transfer to a bowl, cover and set aside, 10 minutes. Peel, seed and dice. Combine with 4 diced jarred piquillo peppers, 1 tablespoon honey, 2 tablespoons canola oil, the juice of 1 lime, 1/4 cup chopped cilantro, and salt and pepper in a bowl; let sit at least 15 minutes before serving.