The Motor Shield (R3) shows a connection for Vin on the Stepper Motor Connector. This connector is used to supply power to the motor when the current demands exceed what can be supplied by the USB. So what this connector should be labeled is VMOT because that is what it really is. If it was simply Vin, there would be no way to separate Vin from VMOT.
By default, VMOT is connected to Vin by a jumper on the reverse side of the motor shield. Since Vin, from what I can tell, is the external voltage input on the Arduino, you should not exceed 12 volts because that's the upper limit of its voltage regulator.