Misfire at cruise, popping/afterfire at 3000RPM

Disconnect the 2 secondary carb linkages and just run it on the center 2bbl. Then test run it up to 3000 rpm again.

If running on the center 2bbl only straightens out your stumble, then you know the engine is working proper and either one or both of the secondary 2 bbls are plugged and they are bringing in a lean condition as they are opening up, adding more air but not the needed extra fuel.

Multiple carbs, multiple problems especially if the vehicle has been sitting for a long time.
I ran it off the center carb only while I was rebuilding the outboards, had the same issue.