I got this idea in my head because I didn't feel that regular clam chowder had enough oomph to it. Adding bacon and Guinness to it does the trick.
After about 10 - 15 minutes, when the bacon is getting crispy, remove it from the pot with a pair of tongs, leaving the bacon grease in the bottom of the pot. Now throw in your diced onion and celery and 2 T of butter into that pot, turning the heat down to medium-low, cooking it until the celery and onions are nice and soft. This will take about 20 minutes. Be sure to stir it occaisionally so that it doesn't burn or stick to the pan.
While that's going on, in a separte pan, you'll want to sauté your clams with your thyme, mustard, salt, pepper, and red pepper in a pan with 1 T of butter. The idea is to cook the clams about half-way (about 2 minutes), so that when you add them into the stock pot they won't get all chewy. As they're cooking, pour in your dry vermouth. When the 2 minutes are up, set the pan aside. You can pour any of the excess clam juice that came with the clams into the stock pot that has the celery and onion cooking away in it.
Next you'll want to chop your potatoes into roughly 1 inch cubes, and put those and 1 bottle (12 oz.) of Guinness into the pot, and simmer for 10 minutes.
Once the 10 minutes are up, you'll want to pour in 8 oz. of the clam juice into the stock pot, and add in your partially cooked clams, and leave the pot to simmer for around 20 - 30 minutes, being sure to give the pot a stir every now and again.
Once the 20 - 30 minutes are up, you're in the home stretch. Add another 6 oz. of clam juice and another 4 oz. of Guinness to the pot, and once the pot comes back up to a simmer, turn the heat down to low.
Take your roux and add a little bit at a time, stirring into your stock pot so as to start to thicken up the chowder and give it a nice velvety appearance. Be careful that you don't add too much roux, in that it will thicken it up so that it's less chowder and more solid - but if you do add too much, you can always thin it out by adding more Guinness to the pot.
OK - now that the roux is incorporated, slowly pour your heavy cream into the pot, stirring as you add it. Now put your bacon back into the pot, and let the chowder simmer for about 5 minutes before serving.
Corn bread goes really well with this.