Place onions in crock-pot. In a small bowl, combine brown sugar, paprika, kosher salt and pepper; mix thoroughly. Rub mixture all over roast and place the roast on top of the onions.
In a medium bowl, combine vinegar, Worcestershire, red pepper flakes, sugar, mustard, garlic salt and cayenne pepper; whisk to combine. Drizzle about 1/3 of vinegar mixture over roast. Cover and refrigerate remaining vinegar mixture.
Cover crockpot; cook on low for 10-12 hours. Drizzle about 1/3 of reserved vinegar mixture over roast during last ½ hour of cooking.
Remove meat and onions; drain. Chop or shred meat and onions. Serve with remaining vinegar mixture or your favorite barbeque sauce.