Hi,
I can't see why the circuit wouldn't work below 4V. If the LED is a white one then I understand but if it's a normal red or green with ~2V forward drop then you should be fine on 3.3V. Besides, the LED is to be replaced by the transistor, right?

Yes, the pulses are still at the full voltage and you are correct that it's something you should take into consideration however I don't think it would be a problem in this case. It's quite normal to run hava a higher power supply voltage in order to compensate for the I*R-drop in the windings etc, I don't think 25% "overvoltage" would be a problem. Do you have a datasheet on the motor?

/Henrik.