I fly F5J as well. How different are the setup? I would simply have a condition for each model where you change what you want changed. This is not unlike what power pilots do with aerobatic planes. A condition for smooth aerobatics and another for extreme 3D. Using conditions you can change just about everything there is in the model.

But answer your question there is no way around re-linking if you want to use two different model in the model select menu.