Stalls in Gear, Automatic- Restarts Good- Can Slam it into Gear! EEEK

no vacuum leaks other than small one at egr

This is probably why you have a rough idle, and need the metering rods raised. The egr valve is likely stuck open, creating a vacuum leak, resulting in a lean condition and consequently, a rough idle. Smack the base of the valve a few times with a hammer and drift punch and see if it idles better. Sometimes that will be enough to unstick it., sometimes not.

And for heavens sake, would someone please get yellow rose some ice cream?:D