The PCM still has provisions for the EGR.
You will need to enable EGR and log the EGR PID.
1999+ LS1 PCM EGR Pin-Out:
Pin 41, EGR Pintle Position Ground
Pin 47, EGR Pintle Position Sensor 5V Reference (constant 5V)
Pin 55, EGR Pintle Position Sensor Signal (WBO2)
In a pinch you can push the wire into the connector
until it makes contact with the PCM pin.
I have done this but I suggest getting the terminals for a solid connection.