Is there any program out there that can let me capture my raw joystick and throttle /keyboard inputs (I have x52 pro) and record that (almost like a flight data recorder) and save it so that I can play it back on a different planes or even different version of flight simulators?

Actually yes. There is a program called "FsRecorder" that does almost exactly that. Make a "recording", and when you are playing it back, you can switch aircraft and still have it work. I am not sure if it is cross-sim platform.