Glad to hear you got it going ... using the 2002 LQ4 / 4L80 PCM tells you that the wiring (adapter harness) is correct for use with a 4L80 tune. Other than some DTCs for the Alternator, Oxygen Sensors, and perhaps the EGR and Air Pump - that tune should work OK for now in your 1999 truck. The Injector Flow Rate is different, so the Fuel Trims may eventually cause DTCs.

The original PCM must have been a 1999, if you were able to install the 2002 PCM - the 1998 truck PCMs had 4 connectors (not 2 like your truck).