A minus number for the MAC% would indicate a very nose heavy aircraft, so either you made an error in modifying the aircraft.cfg so as to move the centre of gravity somewhere it shouldn't be or you are doing something wrong in loading the aircraft.  You should only use the Captain Sim Ace utility to load it.  Or yoo may have forgot to install the replacement air file which I seem to recall moves the centre of lift.

I'm not sure what you mean by the "AP doesn't come up." If you mean there's no popup when pressing shift-4, I guess you did something wrong in modifying the panel.cfg file when you enabled the MAC/TAT gauge.