You could try mapping the controller inside steam as a gamepad. And then launch the project wingman.exe from the steam library.
I use MS Side Winder FF2 joystick with the x360ce for the vibration in afterburner flight because this joystick have forcefeedback. If I open the emulator file again after the game launch this retain mapping axes and buttons (and works good), the 42-55 fps lock disappear but the FFB vibration disappear too. I like have FFB vibration and unlocked fps at the same time. Look like of the x360ce emulator lock the fps to 42-50 fps when vibration is active. And I don't know how fix this.