Cook pasta according to package directions.
Drain pasta.
Add butter and flour to the pot, and whisk until butter is melted and cook the flour for a minute on medium heat.
Slowly add the milk in while whisking, keep adding the milk until it's all incorporated and looks like a sauce.
If you add the milk too quickly it will be lumpy, add 1/2 cup at a time slowly while whisking: trust me, I've been in a hurry and rushed it and wanted to start all over sometimes.
Once all the milk is incorporated, add the cheeses and whisk the cheese into the sauce until smooth.
Pour sauce over pasta.
To top off this dish, I heated the crumbled bacon until it was crispy.
Then topped the Pepper-Jack Mac and Cheese with the bacon, cilantro, and the additional jalapeño.
The large dish pictured is this recipe doubled-two pounds of pasta-which I find is a great amount to bring to a party.