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I have a 98 F150 5.4 engine and I just put Gibson headers on it. Since then it doesn't run right and the OBD II test said there was insufficient EGR. I replaced the EGR Tube and plenty of exhast flow is getting to the EGR Valve. I also find it funny that the EGR system worked fine until I put headers on. Any Ideas what might be causing this???
Was it a code P0401 that you got?
Usually that's caused by a bad DPFE sensor but like banjopicker said it could be the passages in the intake are plugged.
Any chance you missed hooking something up when you installed the headers? Maybe a vacuum hose or something?
If those passageways under the throttle body are clogged, cleaning them will usually restore proper operation. I made the mistake of replacing parts before I cleaned everything out. I guess it was worth it since I had 100K on the truck at the time, but it would have been nice not to spend hundreds of dollars on unneeded parts.
The deposits in mine were so hard I had to use a screwdriver and a hammer to get them loosened up.
I also used a .50 cal wire brush to get most of the rest out.
Good luck!