Lightly grease the insert of a 6-quart slow cooker.
Add the uncooked pasta, butter cubes, cream cheese cubes, kosher salt, and cayenne pepper into the slow cooker.
Pour the whole milk and heavy cream over the ingredients. Stir gently to distribute the liquid.
Cover and cook on LOW for 1 hour. Remove the lid and stir well to separate any pasta clumps.
Cover and continue cooking on LOW for another 30 to 60 minutes, checking every 20 minutes, until the pasta is tender (al dente). Do not overcook.
Once the pasta is cooked, sprinkle the freshly shredded cheddar and pepper jack cheeses over the top.
Stir rigorously until the cheeses are completely melted and the sauce is smooth and creamy. Serve immediately.