I still have some troubles understanding what is going on with your boat. Was it the centreboard case that was too long all the time, or was the bulkhead too far forward and the centreboard case the right length? If the bulkhead was too far forward and you have already cut it out, why don't you glue the new one in the correct position and fix a standard size centreboard case? A bulkhead too far forward and the centreboard case cut short to get the board in the right position must mean that the centreboard will come up through the thwart? That will be a bit uncomfortable while rowing don't you think?
Pontus