Cut bacon into 1/4 inch strips and cook in a soup pot over medium heat until fat is rendered and bacon is crisp. Drain on a paper towel-lined plate and retain bacon fat.
While the bacon is frying, prepare all other ingredients before starting soup. To prepare the clams, drain the juice into a large measuring cup or bowl and then strain through a fine mesh sieve to trap any sand or debris.
If you don't have a fine sieve, line a colander with cheese cloth before straining the juice.
Saute onions (both types) and celery in 2 tablespoons of the rendered bacon fat in the soup pot until tender, about 8 minutes.
Add the potatoes, celery root, parsnips, clam juice, dried thyme, salt and white pepper. Simmer uncovered until vegetables are just fork tender, about 10 minutes.
In a food processor or using an immersion blender, puree 1/4 of the shrimp with 3/4 cup of the cooked vegetables and liquid; add back to the soup.
Stir in cream, milk, liquid smoke, fresh thyme, bacon, clams, fish, and the rest of the shrimp; simmer for 20-30 minutes to cook and meld flavors. Finish with freshly ground black pepper and salt, to taste.
Make-ahead Tips: Chowder freezes well, so if you have a stock pot, I recommend making a double batch.The soup will be very thick once chilled or frozen, but resist the urge to thin it until it is warmed through.Thin with thin with milk, chicken or fish stock, if desired.