DC motor does not work using PWN or Digital pins
The Tutorial.pdf document that describes the components in the kit does not tell you what the current draw of the motor is. Chapter 10 has 2 tutorials on how to use the motor with a relay or L293D IC. This suggests to me that the motor draws a lot more current than a digital output can provide.

The tutorial using the L293D gives you the ability to vary the speed of the motor using PWM, so it would be a good place to start.

Hopefully pin 3 was not damaged by the excess current flow when the motor was attempted to be powered from it.