Give it the 2000 RPM test. With truck in park try to slowly increase engine RPM to 2000 and hold it there, then slowly bring back to idle. If this cannot be done fairly easy, your IP is on the way out.
If you are trying to eliminate the S code EGR see if you can find a F code intake. It will have the provisions for the IAT and MAP sensors I believe the J intake was only on non-turbo engines, pre electronic injection (no provisions for either sensor).