It's a bad idea to connect a motor directly to the I/O. I've attached a little circuit on how to do it with an NPN BJT (like a 2n3904, although I don't know the max current for that). Haven't tested it out myself, but it should work for your circuit.
Few questions I got via email; I was curious about the RTC option, more over the super cap.. I am assuming it replaces a battery, and if so how long will it run the clock when the power is off? Correct, the super cap replaces a battery. The super cap charges whenever Vin over 5.1v is applied (either...