Bring a 3 quarts of water to a rolling bowl in a heavy bottom sauce pan. Salt the water and add the potatoes. Cook just until almost tender, about 10 minutes. Drain well in a colander and set aside.
Cook the bacon until crisp in a 5-quart heavy bottom pot or dutch oven over medium heat. Remove the cooked bacon to a paper towel lined plate. Cut or break the bacon into 1/2-inch pieces and set aside.
Remove all of 2 tablespoons bacon fat from the pan. Add the butter and cook the onions, scallions, corn, thyme and red-pepper in the dutch oven until the onions are tender, about 5 minutes. Add the garlic and bay leaf and sauté for about 1 minute or until garlic becomes fragrant. Add the clam juice and deglaze the pan, scraping up any pieces struck to the bottom of the pan.
Add the half and half to the onion mixture and bring just to a boil over medium heat. Add the potatoes, 2/3 of the chopped bacon (reserve 1/3 for serving), and the salt and pepper. Reduce the heat to medium low and cook the potatoes for about 10 minutes.
Salt the salmon pieces and add to the chowder along with the lemon zest. Occasionally stir gently and cook gently just until the salmon is cooked through, about 5 to 8 minutes.
Discard the bay leaf and serve the chowder topped with chopped chives and the remaining bacon pieces. Garnish with fresh ground black pepper and a good squeeze of lemon juice. Serve with crusty bread for a complete and hearty meal.