I don't know why merging the tail section with the rest of the aircraft fuselage should have fixed your problem. To the best of my knowledge, the only thing that matters as far as rudder rotation is concerned, is the name of the actual rudder part being stated in the aircraft controller.
If you don't want the tail to be one piece with the rest of the aircraft just keep it separated and import it in a new node set as a child node of the main fuselage. If my explaination is not clear enough, just look in stock game for an example of air units that have their rudder rotating correctly AND their tail breaking apart when hit
