Hi Jim,
Don't know about this system in particular but a question I would ask is how does the PCM get the EGR feedback. Also, you have not mentioned checking the vacuum integrity or cleaning the EGR pipes etc. I may be wrong but I would have thought that if the vacuum pump has more than about 25-26"HG (the maximum it can be is 30"HG) and you have no leaks then that should be ok. I would also think that if this was a vacuum issue then the brake servo would be very poor. I hope I've not misunderstood and that this helps.
Regards,
Bryan.