Amass your materials and get a nice space to spread out and work. Start by opening up your controller and begin the preliminary layout of the components. Remember that weight distribution is important, especially with a pistol style controller. you want to make sure that the heavy components, like the battery, are positioned in a way that makes holding the remote comfortable.

Remove the controller's control board. It should be held in place with a couple of screws. Inspect the board and locate the section dedicated to the AM radio. This is usually near or around the crystal and consists of a series of coils, caps and such, as well as an IC. Use a sharpie to draw around the circuitry and either desolder it or cut it out all together. TRY TO PRESERVE AS MANY MOUNTING POINTS AS POSSIBLE. This will be useful later if you choose to use any of the original pots, LEDs or switches. See what I did in the pics for reference.

Desolder all of the wires from the three pins on each potentiometer and identify the polarity of the LEDs you would like to use. I just went ahead and soldered 330Ohm resistors to the back of mine rather than try and repurpose the old SMDs.

Position each of the components where you would like inside of the case and mark each screw point. Using the appropriate sized drill and drill the mounting holes. (After putting on your face protection of course.)

Mount your hardware and solder the appropriate wires from your ADC pads, GPIO pads and other components together. Each build will most certainly be unique so use your discretion as to which component attaches to which Arduino pin. I used the following configuration:

LCD: 4,5,6,7,8,9
Encoder: 2,3
XBee: 0,1
Channels 1-5: A0,A1,A2,A3,A4
Battery Sense: A5

Hook up the power circuitry through the old power switch. In my configuration I use two switches. One is a toggle that is hard wired to the power button on the Portable 5V Power Source and the other connects the 5V output to the Arduino. To turn on the remote you toggle the switch to turn on the Power Source, then slide the old power switch to start the controller. Works pretty well actually. By using a salvage Power Source PCB, you also get the battery charging circuitry, which is really handy. All you have to do is run a USB cable from the charge port and coil it up in the old battery compartment on the remote. When you need to recharge the system, just plug it into a USB port.

Load the code and test the system. At this point both controller and receiver should be powered up in order for the system to operate. The LCD shows live information from the receiver. This way it is apparent when there is a connection issue. You should see the controller position indicators move with the motion of the potentiometers and you should see values for the receiver's battery and current values (this requires a compatible Attopilot style I/V to V sensing device).