In game you need to allow the throttle to use the throttle level rather than key settings by pressing the numpad '/' key.
I think that is the answer to a lot of people's joystick issues. My throttle was mapped to the right axis, but it wasn't enabled in-game... it did need inverted though.
What I am trying to change is the axis used for torso twist. In the config that came with the mod, torso twist is the x-axis rather than the RZ (twist). I managed to get turning to work on the x axis like I wanted, but I'm not sure which line I need to change to get torso twist working. I may have it set correctly, and just need to adjust the dead-zone. Does anyone know which line is vehicle torso twist, or how to add the dead-zone parameter to the line? I'm pretty sure its one of the rotateyaw lines, but there appear to be several in this config file.