I assume the "manual steering rod" you're talking about is the steering cable, and if so it sounds like it's too short. You shouldn't have to trim/cut anything. Also, if that Carolina Skiff doesn't have a tunnel like most all of their boats, why put a hydraulic JP on it other than the setback? Without a tunnel you can only gain maybe 1.5 inches before risking a motor overheat. We've installed tunnels in quite a few Carolina Skiffs, 14 foot to 24 foot with excellent results. It does require raising the transom at the same time to accommodate the higher motor position. Just FYI.

 

At you referring to the transom itself or the rollover or lip in the back above the transom? Post a pic of your transom. I have an old 1860 and I have a roll over on the sides and on the transom to keep water out but if I were to have a 5-6 inch setback, my steering cable would go over that lip and back to the outboard.