Thanks for the schematics.
You have to make some changes.
The led (with the 330 ohm resistor) can be connected to a pin of the Arduino.
You don't need a transistor driver for that.
The 1N4749 has no use at that point, please remove it.
I don't know the HJ A42, what is that ?
The IRF540N is not a logic level power mosfet. Please get a "logic level" power mosfet.
Most mosfets need about 9V at the gate to turn fully on. The Arduino output pin is only 5V (or 3.3V for some boards), so you need a mosfet that is fully on at 5V.
I buy my "logic level" mosfet at Ebay, regardless of the type.
Sparkfun has selected a good and cheap "logic level" mosfet, https://www.sparkfun.com/products/10213
You need a flyback diode over the fan and motor. They are motors, so they are inductive.
Scroll down for the picture "Connect a DC motor" in this ABC guide, http://arduino.cc/forum/index.php/topic,154549.0.html
A capacitor of 100nF is often placed over the motor without resistor.
That ABC guide uses 1uF without resistor. That is also valid.
I prefer 47 or 100 ohm and 100nF, it is called a snubber circuit.
You don't have to use a snubber circuit, but it could prevent RF noise.
The capacitor can perhaps be 500pF to 10uF. It is only to reduce the very short voltage spikes.