Carbon buildup can definitely cause misfires as it increases compression and creates hot spots. Though it'll usually be a symptom more so in a high load situation and you're getting it when the engine is unloaded at operating temp? Either way, the carbon buildup is only symptom of the misfire that you already know is happening. If it was a root cause, it should have lessoned after cleaning.
Sorry you're going through this.
Looking at the firing order 1-8-4-3-6-5-7-2, what is odd is that 4 and 7 are third in sequence. These vehicles are so integrated without a separate ignitor from the ECU. I believe you have already swapped coils around?
Do you have the Ignition noise filters in place on the heads? I doubt that could cause this misfire as I believe it's just to attenuate electrical noise.
Hard to see a pattern in the wiring that ties 4 and 7 together.
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I'm not sure what discoloration you're referring to. Just taking a guess out of left field but I wonder if this engine has been overheated or seen severe detonation before.