Sounds like you're on the right track mate.
A process of elimination.
Something else worth checking is all of your earths, particularly on the engine.
There was a known problem with some ECU's/looms where a faulty earth caused misfiring. I remember reading about it in a Possum Link ECU manual and heard of a couple of people having the problem.
With the amount of time that shell of yours has spent in the weather and a new loom, it could be a simple thing causing you a whole bunch of headaches.

Karl

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