Well as a test, I burned him a chip with just the following changes in constants:
MIN TPS% for EGR 3.1 --> 10
MIN MPH for EGR 0 -->10
MIN RPM for EGR 800 -->1200

He reported back that it made a HUGE difference, and I my guess is that now when EGR is commanded, the engine is beginning to make a little power and is not affected like it was before. He is going to drive it for a week and let me know.