Choosing the correct power supply for my stepper motor (and other questions)

It seems we have a confusion of terminology. When you say pin I think of a GPIO pin, but I guess that you mean the 5V supply (Vcc). Not usual to hear the Vcc output referred to as a pin. If Vcc comes from USB there is about 500mA available from the Vcc output. If powered through the power plug or Vin, the 5V regulator can supply about 1 Watt (current depends on how much voltage the regulator must drop). Powering 3 A4988s from Vcc should be no problem.