Make the soup: Slice the onions into thin strips, cutting from root to tip.
In a large pot or Dutch oven, melt the butter over medium heat. When the butter starts to foam, add the onions and increase the heat to medium-high. Cook, stirring regularly with a wooden spoon and making sure to mix from the bottom to the top, for about 10 minutes; the onions will release their moisture, then slowly start to caramelize on the bottom of the pot.
In a measuring cup, mix together the bourbon, maple syrup, soy sauce, and vinegar. When the onions have turned a golden brown, add a third of the bourbon mixture and scrape the bottom of the pot to release any browned bits. Cook until the liquid has evaporated and the onions begin to brown again. Repeat this process two more times. After the last addition of the bourbon mixture, let the onions cook for 2 minutes to remove the flavor of the alcohol, then add all the stock. Bring to a simmer over medium heat, then cook for 20 minutes, until the onions are soft and brown and the soup has thickened slightly.
Season with the salt and pepper to taste, then serve in deep bowls, each garnished with a cheddar cheese wafer (recipe follows), if desired.
Make the cheddar cheese wafers:* Preheat the oven to 375°F.
Grate the cheese on the largest holes of a box grater. Transfer 4 ounces (two-thirds) of the grated cheese to a large bowl. Add the butter and stir until combined. Add the flour, cayenne, and salt and black pepper to taste.
Transfer the cheese mixture to a work surface. Knead until it forms a dough that holds together when you squeeze it with your fist. Portion the dough into 6 balls.
On a clean work surface, place one ball of dough on a piece of parchment paper and roll it out into a round 3 to 4 inches in diameter. Leave the edges rough. Transfer the round of dough to a sheet pan and repeat with the remaining dough.
Bake for 10 minutes. Top the wafers evenly with the remaining 2 ounces of grated cheese. Bake for another 3 to 4 minutes, until the cheese is melty. Remove from the oven and use immediately as a garnish for the whiskey onion soup or store in an airtight container at room temperature for up to 2 days to enjoy as a snack.
*A cheddar wafer gives onion soup the same crunch as a toasted baguette but with cheesy flavor. I like these wafers so much, I make them even without the soup, just to eat as a snack. Make sure to use good-quality cheddar and shred it yourself. Don’t use pre-shredded cheese, as it will not melt correctly.