Cook the chopped bacon in a large skillet over medium heat until crispy. Remove bacon with a slotted spoon and set aside, leaving the rendered fat in the skillet.
Add olive oil to the skillet if needed, then sauté shallots and garlic until fragrant and translucent, about 2-3 minutes.
Add sliced mushrooms and cook until browned and their moisture evaporates, about 7-8 minutes.
Sprinkle whole wheat flour over the mushroom mixture and stir well to combine. Cook the flour for 1-2 minutes to remove the raw taste.
Slowly pour in the dry red wine, scraping the bottom of the skillet to deglaze and combining it with the flour and mushrooms.
Add the water and chicken stock, stirring constantly until the sauce thickens slightly, about 5 minutes.
Stir in the diced tomato and fresh spinach and cook until spinach wilts, about 2 minutes.
Return the cooked bacon to the skillet and mix gently to combine and warm through.
Season the sauce with black pepper to taste.
Cook whole wheat pasta separately according to package instructions, then drain.
Toss the cooked pasta with the mushroom and bacon sauce until evenly coated.
Garnish with chopped chives and torn basil leaves before serving warm.