First, having the Fire Guns in the rudder is an oddity that can return after some update or other major event like a brownout of the USB ports. It's rare but common and easy to cure if it happens again.
Did you also calibrate the toe brake movement in the game? If not, it'll be off-on only. The toe brakes should be assigned as Analog Brake Right and Left to the X and Y axii of the pedal and the rudder as Analog Yaw to the Z axis. You should see numbers running when you move any of them in the basic view. If not, use the Calibrate button. By checking Advanced you can further investigate and adjust if needed.
Last but not least don't forget to press OK to save your settings! Clicking Back is quite easy but it won't save anything.
