Well, we finally got this car to stop throwing codes and it passed e-check!!! This whole process was confounding, and I am still not sure if it had multiple problems or if I kept missing the actual problem.
Here is the chronology of the problems / codes and the solutions. The first code was P0402. I had done the vacuum line reroute on my '99 and failed to remember that my code had been P0401. So I moved the vacuum line from the top of the intake by the TB to the back of the intake. The previous owner had already moved the line from the OEM port to the top. So when it threw a code again, we took off the top half of the intake and cleaned out the EGR passage. Unfortunately we didn't check the code until after we did the cleaning. Turned out that the code was actually P0420 which is Catalyst something. We decided to clear the code and see if it came back, thinking that it might have been caused by the throttle body cleaner that we used to clean the intake.
The CEL came back on and we checked the codes again. This time it was P0171 which is a lean condition. I added P0171 to P0420 and added Keith's advice and figured it had to be the O2 sensor. Replaced the O2 sensor and was SURE that we had fixed the problem! A half hour later the CEL came back on.
Last night we got the car back to my shop and it was throwing P0171 again! Since the O2 is new what is left? When I lifted the hood you could hear a loud hissing! I swear that it never made that sound before!!! The OEM vacuum line port for the EGR was leaking. The PO had capped it of with a cap that had a split in it. New cap, no leak, passed e-check.
I think that the port was so clogged that it didn't leak until after we cleaned out the EGR passage. I really don't think that this leak was the problem all along, but it was the final piece to the puzzle.