I'd start with the EGR system too. The CA emissions rigs used a different computer, and an extra thermal switch on the EGR valve. If you have the FED version (check the ECM label) you might have to "fiddle" to get it past.

As for the idle, it's possible that the throttle body may be worn/dirty. When you had the motor apart, did you clean out the air bleed ports ? Did you check that the manual throttle stop was properly adjusted ? (that's the screw on the front of the throttle body, that _usually_ has a dab of red paint on it) You probably already know that screw isn't used for setting the idle speed, and the one on the rear side is. I imagine the TPS could play a part too...