From an electronics standpoint if all you are trying to do is bypass the current speed controller and install one like the amp flow there are a few ways to do it.
according to this page
http://www.battlekits.com/controllers.htm
The ampflow speed controller can be controlled in a few different ways.
R/C Radio mode
R/C Radio is the most popular, simplest and least expensive method to build and operate a remote controlled robot. The controller supports many configurable options, including joystick calibration of min, max and center positions and dead band adjustment. Full optical isolation is provided on all R/C control inputs. This method requires the generation of PWM (pulse width modulation) signals which can be created by any standard RC receiver or a robotic based micro controller(like those we use in FIRST).
Serial Port (RS232) mode
The controller may be interfaced to a microcomputer for autonomous operation. More advanced operations are possible, including remote control via the Internet, using a wireless modem or wireless network adapter. This method is more straightforward for using any micro controller. If you were to wire your joystick to the controller which interprets the potentiometers within the joystick you could do this.
The last method will seem to be the easiest.
Analog mode
A simple 0-5V analog control mode is also provided for direct connection to potentiometers or joysticks. You hardwire the potentiometers in your joystick to the controller. Obviously you will have some calibration to do, but according to the documentation for the speed controller this doesn't seem to be too hard.
Typically I would just end this with saying "good luck with your project" but something inside me requires me to say "be safe with your project" also that any information provided here is for reference only and Myself or chiefdelphi can not take responsibility for your actions based on recommendations in this post. So please be safe and good luck.