So, I managed to patch into the controller for the joystick and took a quick video to show progress.
The hardest part of this so far was using the wrong set of transistors (Which are being used to digitally simulate a button press on the controller). I was using medium power, when I needed to be using the BC108 low power transistors.
This is because the switches on the controller itself are going off 3.3v, and I was trying to switch them using a 5v signal from the arduino. I swapped to low power transistors, and threw in a resistor to reduce the voltage going into the transistor, and now it works a charm.
I also wasted a fair bit of time digging out the spec for the joystick from the archives of the internet, which basically tells me, I need to look for an easier way to control the motors than trying to replicate the joystick itself.
See the spec for the joystick here:
More progress soon I hope.