In a large pot, saute the bacon until translucent.
Add the onions and celery, and saute for 5 minutes. Pour in the juice from all of the clams (setting the clams aside). Pour in the bottle of clam juice too. Add the potatoes, thyme and pepper. Bring to a boil, then turn down to a simmer; simmer until the potatoes are tender (about 10 minutes).
In a separate small saucepan, melt the butter over medium heat. When the butter is bubbling, whisk in the flour to make a roux (your thickening agent for the chowder). Turn down the heat a bit, and continue to stir and cook the butter/flour for about 3 minutes.
When the potatoes are tender, add the chopped clams and simmer for 2 minutes. Stir in the roux, and continue to simmer for another 5 minutes.
In a separate saucepan (or in the microwave), heat the cream until just before boiling. Stir the hot cream into the chowder base. Remove from heat, and let sit for a bit to cool down some. Taste to see if you would like any added salt.
Serve individual portions with oyster crackers, sourdough bread and maybe even a pat of butter on top. Sprinkle crispy bacon on top too.
Notes
If you are preparing this recipe as gluten-free, substitute sweet rice flour for the all purpose flour when making the roux.