In a large Dutch oven cook bacon over medium heat until crisp. Remove to paper towel lined plate.
Add shallots, peppers, salt, pepper and cayenne to Dutch oven and cook over medium-low heat for 15 minutes, until softened. Add the garlic and cook for 1 minute.
Add wine and continue to cook until almost evaporated.
Add the thyme leaves and clam juice and bring to a boil. Lower the heat to a simmer and cook for 20 minutes.
While soup is simmering, melt butter in a small pan over low heat. Whisk in flour and cook 2 minutes, being careful not to burn. Whisk in one cup of hot clam juice. Add mixture to pot.
Add milk and clams and continue to cook until thickened.Add bacon.
While soup thickens make toasted bread crumbs:
Melt butter in medium saute pan. Add breadcrumbs and cayenne and toss to coat. Continue to toss until crumbs are lightly browned.
Serve soup in bowls and top with toasted breadcrumbs.