Just thought id update my experience with this.
I've had my egr deleted per "joesperformance" instructions and it worked flawlessly. I capped the bung on the exhaust manifold, left the valve where it was, and moved the vacuum lines off the valve and back to the reference port.
No check light, no studder, and mpg has been restored. Big thanks goes out to joesperformance for helping me get that straightened out.