Ok, to clear the KAM you have to disconnect the battery and create a draw (turn on your headlights, for instance). This will deplete the capacitors much faster than their normal half-life. I do this and let it sit for a couple minutes.
You have found an issue however. At idle, the EGR's vacuum line should have NO vacuum in it. 2.5" hg might not be enough to really trash the idle, but you should be able to notice it. It should also cause off-idle surging.
If you disconnect the vac line to the EGR and plug the line, does it still surge? If you go for a test drive, Drive it easy if you do this because you might get detonation (depending upon if the EEC has shut off the EGR function at that time).
Alternatively, trace the vac line and be sure it goes to the EVR (in the passenger fender well. YOu remove the wheel and fender liner to access it). Your EVR might have a leak, causing manifold vac to bleed across the ports.