First, shred your cheese (you’re looking for about 3 cups total), dice jalapenos and bacon, and measure out half & half, pasta, and flour.
Heat deep saute pan over medium heat. You’ll build your cheese sauce in this so make sure it's large enough. A large pot works well too.
When saute pan is hot, add diced bacon. Heat 8 cups of water in a second large pot over medium high heat.
Cook bacon until crisp and browned then remove from pan to paper towel. Drain all but around 1 1/2 tablespoons of bacon fat from pan. Give the bacon fat a chance to cool for a few moments off heat*.
Check your water, if boiling, add a palmful of salt to the water, and add pasta once salt has dissolved.
Return the bacon fat to medium low heat. Begin with 2 tablespoons of all purpose flour and add to remaining bacon fat. Whisk, adding more flour as needed until a blonde paste has formed. Cook for 2-3 three minutes, whisking frequently until smooth and creamy.
Add half and half in thirds, whisking between each addition until creamy. Add diced jalapenos.
Continuing to whisk, return the heat to medium, bringing the half & half to a boil. Simmer and whisk mixture until smooth and thickened.
Remove pan from heat and add in the cheese in handfuls, whisking each addition in before adding more.
Drain your pasta, reserving 1 tablespoon of pasta water, and add all to the cheese sauce. Fold to combine.
Add in the bacon and stir in. Taste, add pepper and salt as desired. Serve!
Notes
* Adding the flour to a too hot pan will cause the roux to burn