Z-step pulses too short (Marlin 2.0.x)
By avoiding pin 3 entirely, the Z-axis steppers have started to move correctly. My bed heater went out a while ago, so I redefined the connections in Marlin to use that pin (pin 12) as the Z-step pin, connecting it to the A4988 accordingly. This has caused no issues other than small noise problems so far. Unfortunately, I can't speak to any potential issues pin 3 may have had to cause this behavior, all I have is this one potential solution.