I finished this prototype today and mounted everything on a permaboard.  I updated the code to include two triggers, either triggered from the buttons on the board, or a TRRS input jack.  Here is the final design working.  The pellet dispenser has two inputs.  When the first is triggered it attempts to dispense a pellet until it detects one with the photo-interrupter.  When the second is triggered it moves a servo to open a trapdoor to remove the pellet.

The Neopixel on the Adafruit Feather M4 also displays some status information:

Green: All good, monitoring inputs

Red: Dispensing

Blue: Moving servo

Green with red flash - Pellet dispenser encountered a jam and needed to clear itself

The next step is a custom PCB! here's a sneak peak: