Preheat oven to 375°. Cut squash in half lengthwise and use a spoon or melon baller to remove seeds and surrounding fiber. Put squash, cut side down, on a lightly buttered baking sheet and bake until tender when flesh is pierced with a fork, 30 to 40 minutes. Or poke several holes in skin of squash with a fork and microwave it on high 10 minutes. Squash should be tender when pierced with a fork; if it isn't, microwave on high in 1-minute intervals until tender. Let sit until cool.
Meanwhile, in a medium saucepan over medium heat, warm milk and jalapeños until bubbles form along the edge of the pan. Remove mixture from heat and let sit 15 minutes. Strain and discard jalapeños.
When squash is cool enough to handle, use a large spoon to scrape the strands out of the skin and into a large bowl.
In a medium saucepan over medium-high heat, melt 2 tbsp. butter. Whisk in flour and salt and cook, whisking, until flour smells cooked (like piecrust), about 3 minutes. Slowly pour in jalapeño-infused milk while whisking. Reduce heat to medium and continue whisking until mixture thickens slightly, about 3 minutes. Pour mixture over squash and stir to combine. Transfer mixture to a buttered 2-qt. baking dish. Sprinkle with jack cheese and bake until bubbling and brown on top, about 30 minutes.
Note: Nutritional analysis is per serving.