Did you ever check the pushrods for straight? Rolling them on a flat piece of glass will expose any that are bent. Looks like #4 exhaust is maybe hanging open letting exhaust in, blackening that valve. That would explain the popping if that exhaust was open when #6 was firing. If the nick in #2 is leaking, that would explain both. With rockers installed wrong, it might have limited their travel. You might want to check them for marks on the flat side where they might have hive around the valves. If #2 intake wasn't opening, I wouldn't expect much compression, and if it was hanging open, you would have no compressed fuel to burn.
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