If the temps were close with the cowl off, then it would seem to be an airscrew induced lack of airflow through one side, the screw effect of the airflow will hit the cowl inlet holes in an upward incline on one side and a downward incline on the other, if the inlet holes are radiused or sharp on either the top or bottom this would make a difference to the flow of air into the cowl according to the turbulance created by the prop wash between the prop and cowl, so according to what cylinder is being cooled more, look at the other side to establish the correct inlet hole radius or edge, it may be that the baffles are preventing air flow also.

Mike