If a previous owner has twisted the shafts to correct airflow between cylinders it should be reasonably obvious by either measuring the edgle of the butterfly to carb face or putting a light behind the carb and seeing any difference between butterflies in the two throats. Obviously you will need to take the carbs off to do this.
If this is the case, you could try and twist the shafts back to something close to the same, or buy new shafts.
I think that if you need to correct flows, and do not have an air bypass, I'd personally be inclined to try small drill holes in the butterflies away rather than twist the shafts. Twisting the shafts will screw with the progression holes, whereas holes through the butterflies (as long as they are away from the progression holes!) wouldn't be as bad? Anyone agree with this?