Preheat a stockpot over moderate heat, add oil to the pot, then toss leeks, fennel, garlic and sweet potato in oil to coat. Season with black pepper, salt, and red pepper flakes. Stir occasionally to prevent burning, cooking to soften and brown slightly.
Using a blender, puree the roasted red bell pepper with the tomato puree. Add bell pepper and tomato puree to the pot to deglaze. Bring to a simmer and allow it to reduce and darken slightly before adding the stock. Over the stock pot, stain off the juice from the canned clams, combining it with the red pepper and tomato puree. Retain the clams for later use.
Bring to a boil, then reduce to a simmer. Continue to cook uncovered until the potato is fully cooked. Add the clams in shell to the pot and cook until the clams open on their own. Remove from heat and stir in the retained clams from the can.
Taste and season with additional salt and pepper as needed. Garnish with fresh fennel fronds and serve hot.