The green indicator is serial as you suspected, and I have likewise found it to be somewhat inconsistent; however, when you upload code, the yellow-orange RX LED on the other side of the chip should flash in a specific pattern before the blue power light next to the MicroUSB port comes back on.
If you haven’t tried already, Brandon had previously suggested changing serialEvent (line 196 of RS485_FLUIDICS) to the code below and submitting the commands via USB through the Arduino serial monitor. The fluidics is more confusing than some of the other parameters, but you should be able to just copy and paste in the examples at the top of the sketch into the Arduino Serial Monitor and see if you can control the pumps.