Cook the jumbo shells in a large pot of boiling salted water. Aim for "al dente"—they should be pliable but still have a firm bite. Drain them and rinse immediately with cool water to prevent them from sticking together.
In a heavy skillet over medium-high heat, brown the ground beef until completely cooked through. Toss in the minced garlic and smoked paprika during the last 60 seconds of cooking to release their oils without burning. Drain any excess fat.
Lower the heat to a simmer. Fold in the softened cream cheese and salsa, stirring continuously until the mixture is velvety and the cheese is fully integrated into the beef. Take the skillet off the heat and let it rest for 5 minutes; this makes the stuffing process much easier.
Lightly grease a large baking dish. Using a small spoon, generously pack each pasta shell with the creamy beef mixture and line them up in the dish like little soldiers.
Blanket the stuffed shells with the grated Pepper Jack. Bake at 350°F for 18–20 minutes. You want the cheese to be bubbly and the tips of the pasta shells to have a slight, golden crunch.
Before serving, hit the dish with a fresh squeeze of lime juice and a handful of chopped cilantro to elevate the flavors.