You will need a tool with bi-directional controls like HPTuners, EFILive, or a Tech-2. Generally speaking, anytime the PCM is replaced or the physical relationship between the crank and the sensor is altered this procedure needs to be performed. There are directions in the help manuals of EFILive and HPTuners.
Put the vehicle into park (auto) or neutral (manual).
Turn off all accessories and A/C.
Apply the parking brake.
Press the brake pedal. Keep the brake pedal depressed during the entire procedure.
Gradually rev the vehicle to fuel cutoff (around 4000-5000 RPM's) over a period of about 4 seconds. When fuel cuts out, immediately release the throttle.
Allow the engine to come back to an idle.
Turn the ignition off for at least 15 seconds. This step is required for the VCM to store the newly learned configuration.