Did you tee the EGR actuation vacuum line to monitor vacuum or hook directly to vacuum supply to the EGR valve?

System monitors EGR vacuum and will likely react differently if the vacuum supply is not connected to EGR valve. System modulates EGR vacuum solenoid on/off/on... to obtain a certain change in manifold pressure.

good luck

 

I'm trying to understand your set-up, since on my '99 the EGR is mounted on the intake mani and there's a exhaust port going into it. The ECU controls opening and closing it.
Where is yours installed? You said you have a vac line from the intake plugging into it? How does it connect to the exhaust?