Cook bacon in a skillet until crispy and remove, saving the fat (chop bacon when manageable). Add shallots, garlic, and red onion into this, with a tablespoon of butter and sautee for about 5 minutes. Add clam liquor, potatoes and thyme with 1-2 cups lobster stock and simmer at low heat to create a broth.
Rapidly reduce 3 cups lobster stock over medium-high heat in a separate pan. When this 3 cups of lobster stock has reduced to 2 cups, whip 2 tb butter into it with a wire whisk and continue to simmer down to 1 cup.
Add reduced stock into broth mixture with chopped clams, crispy bacon and let it all get to know each other until simmering nicely. Pour in cold milk and bring to heat but do not boil. (The 2% milk or even fat free evaporated skim milk is a trimmer substitute for the usual fattening cream found in chowders!)
Throw in some freshly ground black pepper and some white pepper to finish it off and let your chowder sit off heat for at least an hour before reheating and serving. May be refrigerated up to 2 days.