Assuming the throttle cables are adjusted the same, and both engines have the same pitch and style of prop, I would run a compression check on both engines. If the compression is similar on both engines I would install a spark checker and check for spark on all cylinders. When you have spark on all cylinders, check the timing at idle and WOT. When you get this far and don't find the problem let me know and we will have more things to check.
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