I'm not an engineer, but that would seem to me to be your problem. The mast end of the boom was raised, so now when you raise the main, the leech of the main is still the same length, so it won't lift the aft end of the boom to be level with the mast end. The sail probably should have been re-cut to work with the new configuration.Some where along the line the boom gooseneck was moved up higher on the mast.
For head room?
Thoughts?