I am having a hard time believing a malfunctioning EGR is causing the crazy spike I was seeing in NOx. Sure, EGR will reduce Nox but that much? I have known CO trucks to get through emissions with EGR disabled so I don't think that is my main issue. Sure, EGR could get me through but that may just be a bandaid.
Likely a combination of things causing that high of NOX levels. Getting everything hooked up and working correctly, along with setting the timing back to stock, should get the NOX levels down.
Did you pull the egr valve and clean the piping? The small stem pipe usually gets packed with carbon. If it is clogged don't try to remove it, they tend to snap, best way is to use a small drill or wire and work out dig out the carbon. Spraying/dripping carb cleaner, seafoam, or gas on the carbon will help it break it up some.
Also check for any cracks in the intake plumbing, under WOT the cracks could open up allowing unmetered air in, the accordion elbow is usually where the cracks occur.
