You didn't state the obvious ones, so:
Did you check chain alignment between front and rear sprockets? And by this I mean check using a straight bar method for chain alignment, not using the marked notches on the swing arm.
Is the chain is lubed well?
Break-in noise does sound plausible until the assembly "runs in" but chain mis-alignment sounds more likely.
Do you have the old sprockets? Check them for thickness and compare to the new ones.
Is there a shim or a shoulder on the front OEM sprocket?
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