I've done quite a bit over the last month with the truck, so I'll give you the low down -
The truck's original owner had the headers and chip done probably in the early 90's. (not sure) The guy I bought it from was the second owner and didn't know very much about the truck. He owned it for 10 years and let his wife drive it. All he said was that he blew a head gasket once and that he thought the car had a chip in it.
After buying it, I changed the oil and plugs, cap and rotor. And ran over to the emissions testing station as you can't transfer titles without passing the test in AZ. I failed HC, CO, and Nox. Also failed the evap test. I replaced the plug wires and at that point the distributor module died on me. I replaced that and the pickup coil, and remote ignition coil just to be thorough as the car needed a major tune up anyway. I swapped the canister out for a new one. I also had the 2 magnaflow cats put on and set the timing at 4btdc. I bought an o2 sensor but forgot to put it on the truck and went and failed my second emissions test. HC, and CO were worse and I passed the Nox and evap this time. I put the o2 sensor on tonight. This brings me to why I am even looking at the chip. My issue is that I need to pass smog LOL!
Thanks for your help so far Jim. As far as I know, the internals of the engine are stock. The throttle body is stock. It squirts plenty of fuel. I need to check the EGR but after that, I'm not sure what else could be causing the emissions failure.