The second post that kongorilla pointed to provided a solution to getting the app to recognize my serial ports. Basicallly, it appears that the RXTX library only looks for serial ports with the names of /dev/ttyS##, while the Arduino's will either have serial ports of /dev/ttyACM# (newer models) or /dev/ttyUSB# (older models and most clones).
By issuing the command(s) from the post above like so
sudo ln -s /dev/ttyACM0 /dev/ttyS40
sudo ln -s /dev/ttyACM1 /dev/ttyS41
sudo ln -s /dev/ttyACM2 /dev/ttyS42
sudo ln -s /dev/ttyACM3 /dev/ttyS43
sudo ln -s /dev/ttyUSB0 /dev/ttyS50
sudo ln -s /dev/ttyUSB1 /dev/ttyS51
sudo ln -s /dev/ttyUSB2 /dev/ttyS52
sudo ln -s /dev/ttyUSB3 /dev/ttyS53
The controller application will then recognize when a serial port is occupied by an Arduino.
Right now, I am using an Arduino Mega an Adafruit V2 motor shield since that combination allows me to have all features on a test bed that should work. Ultimately, I plan to make use of a Chipkit UNO32 to replace the Mega if I can get it to work (I have had it laying around and don't really use it), or I have picked up two UNO sized clone boards that use a 1284 chip that has more than enough flash for all of the code, plus it has more ram memory than even the Mega. Either option will allow me to play with the firmware without concerns about memory.
Right now, I have verified that the controller software will raise and lower the pen servo, as well as turn the main servos. I just need to walk through your instructable on setting up the proper configuration before I run my first plot.
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