Preheat smoker to 220 degrees F. Quarter the onion, and place on the smoker grate. Place the whole leek, and the 2 whole celery sticks on the smoker grate.
Open the cans of clams, remove the lids, and place the cans directly on the smoker grate. Don’t drain the clams. You need the juice for the chowder.
Smoke for 45 minutes. You aren’t cooking these ingredients. You are just adding smoke flavor. This is a good time to cook the bacon, in a frying pan on medium heat. Set the bacon aside.
Remove the vegetables from the smoker. Dice the onion and leek. Slice the celery into small half-moon chunks.
In a large soup pot melt 2 Tbsp Butter. Add 1 Tbsp of the bacon grease. Add the diced onion, diced leek, sliced celery, and minced garlic. Cook until the onion is translucent.
Cube the red potatoes and add them to the soup pot. Add the broth. Bring to a boil, then simmer for 10-15 minutes, or until the potatoes are fork-tender.
Add the clams, with the clam juice, to the chowder mixture. Add the salt, thyme, and bay leaf.
In a small mixing bowl, whisk together 1 cup of half and half with the flour until smooth. Slowly pour this mixture into the chowder as you are stirring. Add the last cup of half and half slowly while stirring.
Chop the cooked bacon up into small bits. Add all but about 2 Tbsp of the bacon to the chowder. Let cook on low heat, without boiling for 2-3 minutes, or until it reaches the desired thickness.
Serve in bread bowls, or normal bowls. Top each bowl with a small sprinkle of bacon bits. Enjoy!