Andrew,
I am not an expert and have not rebuilt an engine myself. After reading your post I consulted the manual UC-F1 and it states "The bolt holes in the camshaft flange are unevenly spaced to prevent improper assembly of the gear to the shaft" Once you get the right orientation of gear to shaft then you would just have the two timing marks to worry about. Would that keyway allow you to turn the camshaft? If so, you may not have to disassemble to valve train to sort out the timing issue.
Again, I am not an expert.
Colin
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