Welcome to cayenne community @andrewjmavor. your project sounds interesting and would love to help you automate using cayenne.
it would be great if you can PM me some of your knowledge on farming (especially microgreen) 
and also automate together to get the best yield from the crop.
as you are able to get the PH and EC reading on Arduino you can send the data to cayenne by using just a single line Cayenne.virtualWrite(channel_1, PH_value, "soil_ph", "null"); and Cayenne.virtualWrite(channel_1, PH_value, "analog_sensor", "null"); here is example code https://github.com/myDevicesIoT/Cayenne-MQTT-Arduino/blob/master/examples/Sensors/GenericAnalogInput/GenericAnalogInput.ino
to send this data to PI you will have to get node-red running on the pi and subscribe to the arduino values and then make the decision. here is a tutorial to get started with node-red and cayenne Using Node-RED as a Local Fallback Server