Place cut potatoes in a bowl of cold water. Cover with plastic wrap and refrigerate, 8 hours to overnight. Remove from water and dry on paper towels.
Heat oil in a deep-fryer to 300 degrees F (149 degrees C). Fry potatoes in batches until tender but not crispy, about 3 minutes. Drain on paper towels.
Preheat the oven to 200 degrees F (95 degrees C).
Turn deep-fryer heat up to 400 degrees F (204 degrees C). Fry potatoes in batches until brown and crispy, about 3 minutes more. Drain on paper towels and transfer fries onto a baking sheet; place in the oven to keep warm.
Heat a large skillet over medium heat. Cook and stir ground beef in the hot skillet until browned and crumbly, 5 to 7 minutes. Drain and discard grease. Return beef to the pan; add onion and jalapeno. Cook and stir until onions are translucent, about 5 minutes.
Stir garlic into the beef mixture and cook until fragrant, about 1 minute more. Add water, cumin, sea salt, paprika, black pepper, 1/4 teaspoon garlic powder, 1/4 teaspoon chili powder, red pepper flakes, onion powder, and oregano. Mix well, turn heat down to low, and keep warm.
Melt butter in a small saucepan over medium heat. Add flour; mix until lightly browned and bubbling, 3 to 5 minutes. Increase heat slightly. Add milk slowly; cook and stir until milk bubbles and thickens enough to coat a spoon or whisk, about 7 minutes. Reduce heat to low. Add cheese in handfuls; mix until melted completely, about 3 minutes. Add remaining garlic powder, chili powder, and 1/4 teaspoon salt to the nacho cheese sauce; mix well.
Place fries on a plate. Pour nacho cheese sauce over the fries and layer taco meat on top.