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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).
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You can't segment swap a 2002 trans segment into a 99 OS...that's probably why it didn't work...it probably didn't copy anything to begin with. You can only segment swap (most of the time) when you have the same base OS.
There have been some occasional post production OS replacements from GM to solve TSB issues, and in some of those instances, while the OS changed, some segments did not...and in those cases, all of the segments can be used with either OS...but that's very rare.