What is not working right?
94 through 03 engines are the same contrary to what some people think.
The differences are the sensors/configurations from the years. California vs. non California.
Hopefully you still have the e99 engine as it came out of the truck. You need to transplant the e99 stuff to the 02 motor first off. DO NOT start changing the PCM.
THAT IS THE LAST THING YOU WANT TO DO!!!
It sounds like a simple wiring miss match, not a big deal.
I have done swaps 10 years and have never had a problem. Have put MANY T444e motors into blown up trucks, hardest part of that is the oil pan change.