Darkness in a manifold isn't necessarily rich/lean. It's gas reversion. The clean areas are where fuel has washed the deposits away. That's why one side of the bores in the center are clean, but the other side is still dark. I wouldn't make guesses about rich/lean based on the color inside the manifold. The sparkplugs are present for combustion, so rely on them instead.
I can't remember, have you pulled the valve covers and looked over your preload/lash to rule out a cam failure?
Dark spark plugs can indicate rich, but can also be impacted by timing and plug heat range. With a misfire situation, you're looking mostly for differences. The observation about the dull header pipes is a good one. I'd be looking there for signs of a cam failure (by pulling the valve covers and looking at lift/lash/preload) or for a bent/missing pushrod, or looking for stuff that could have caused excess fuel delivery. The sticking throttle plates might be a partial contributor there somehow, but I'd be looking deeper into the carbs to rule out other issues (float height, power valve condition, etc).
