As the title says, I found a solution to my joystick problems. The issue at hand is that the inputs unity reads are based on the raw output of the joystick, not the calibrated input. This means that even though I had calibrated the X-45 I just bought, the throttle was inverted, didn't go to 0, and my stick was being read as back and left at all times.
In the past I have used PPJoy to get around this, but I couldn't seem to get it working on Windows 10. I have found a replacement in 2 outside applications.
First is Vjoy. This was originally meant to be a PPJoy replacement, but they seem to only be developing the back end, and letting others create what they call Feeder applications. However I found someone had written a feeder application called Universal Joystick Remapper. UJR takes the windows modified inputs of a physical stick, and feeds them to the Vjoy virtual stick.
So my solution has KSP reading the Virtual joystick created by Vjoy, which is fed inputs from UJR, which takes the calibrated output of my stick.
The result is perfectly stable control inputs in the game. I hope this helps, I've spent about 12 hours researching this. However I can't tell you how disappointed I was when I thought my new joystick would never work in this game. I hope this helps someone else in the same boat.
Vjoy can be found at http://vjoystick.sourceforge.net/site/
and UJR at https://autohotkey.com/board/topic/89279-
