Hi Nick,
It looks like you did a beautiful job with the boat. Before you go changing things radically I would experiment with a fixed skeg. A 18" long wedge of wood tapering from 1" at the stern to nothing at the bow will add a lot of tracking. Place the back end about 18" from the stern. You can just duct tape this on initially, test it out and then secure it more permanently if you like the results.

I'm not sure why your boat is giving you so much trouble. It may be the cockpit location is a little off due to your modification of the length. Making it shorter will often make a boat looser in tracking so when you have an already maneuverable boat, you may end up with something a little too easy to turn after shortening it.

I would give the skeg idea a try before doing anything else.