Bring a large pot of water to a boil. Make sure to cover it, so it comes to a boil faster.
Place a medium-size bowl inside a larger bowl filled with ice. In that bowl, place the Littleneck Clams (3 pound). This will keep the clams cold as you clean them.
Using cold, running water, scrub any grit from the clams using iron wool. and return them to the bowl. Once all done, return to the fridge.
Mince the Shallot (3) and Garlic (3 clove).
Deseed and mince the Jalapeño Pepper (1).
Add Kosher Salt (2 tablespoon) to the boiling water along with the Whole Wheat Linguine (1 package) and cook for 5 minutes. When the linguine is done, scoop out 1/4 cup of some pasta water for later.
Drain the pasta and toss with Olive Oil (1 tablespoon) in a medium bowl. Set aside.
Slice the Bacon (3 slice) into 1/4-inch strips. Into your 5-quart saute pan, add the bacon to the pan along with a splash of olive oil. Cook until crisp and golden.
Remove the bacon using a slotted spoon, and set aside on a paper-towel-lined plate. Add in the Butter (2 tablespoon) and melt.
Once the butter has melted, add in the shallots, jalapeno, garlic and Crushed Red Pepper Flakes (1 pinch).
Add the Tomato Sauce (1/3 cup), Chicken Stock (1/2 cup) and pasta water. Mix well. Place the little neck clams over top.
Cover and cook 5 to 8 minutes until the clams have opened.
Add in the cooked linguine and toss with the clams.
As the clams cook, wash and chop the Fresh Parsley (1 handful). Wash and zest the Lemon (1).
Add the bacon back to the pan, and sprinkle the parsley and zest over top.