I didn't understand your last point about the aditionnal joystick axis needed. Do you mean for orienting the noozles or for controling their thrust ?
For orientation, you could use the keyboard or a gauge. I think that even in the Harrier, all the nozzles are oriented with one command only.
We could use anything, just like I don't know, the commands for the concorde noze for example.
Then for the thrust, a simple gauge that would read the input of the joke, and act on each engine accordingly. For example, if you push you joystick forward, then the gauge reduce the thrust of the two forward engines. If you push it forward-left, then reduce the thrust only of the forward left engine. This would cause the plane to dive in a direction or another.