I was able to expand the GUI to talk to two serial ports at once. I have the Arduino reading the serial encoders on COM10, and the Arduino with the motor shields on COM11. Both Arduinos print back their coordinate to the serial port.
The positions are read back from the Arduinos to the GUI display. The buttons fire off HPGL PR commands to the Arduino HPGL interpretor. w00t!
The machine moves, the encoders increment.
Next step is to add some flow control to the GUI and the ability to spool in a large HPGL command in small chunks so as not to overflow the Arduino serial buffer and give it time to move from point to point.
The code is getting pretty long to post, so I'm setting up a download site
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