After a few rounds of tweaks, the pellet dispenser is operating pretty reliably!  I also added the photointerrupter for detecting when a pellet is dispensed.  Video below shows the current build.  The code (running on an Adafruit Feather M4 express) will turn the stepper 1/8 rotation forward (this is the distance between holes on the pellet disk) and 1/32 rotation backwards, and repeat this movement until it detects a pellet through the pellet tube.  When a pellet is detected the device will pause for 5 seconds.  In the final build it will dispense under external TTL control.

Next up, going to add a servo to clear pellets out of the pellet dish if they're not taken within a period of time!