Damian:

You do need to cut the ailerons off and start over.

CA hinges should be fine, but they do need to line up with each other down the length of the aileron. Cut the new hinge slots wherever you can make them line up properly. When you seal the hinge gaps, you only need to do one side. Most people do the bottom. Use the thinest tape you can or use clear Ultracoat.

The front of the engine should point off a little to the right (looking from the back of the airplane) to compensate for torque, P-factor and spiral propwash. This is a good thing. If it points off to the right when looking from the front of the airplane, you need to fix it.

Rudder slack? No, that won't cause your problem. Rudder stiffness (like the ailerons) could.

Jim