the EGR spacer does not have any vacuum lines to it. The 2 nipples on the spacer are for coolant flow. One of the heater core lines should have a hose running into and out of the egr spacer. It's a popular thing to do (plug off the line) and shouldn't impact driveability, though there are differing opinions as to whether it's a good idea.
As far as your idle issues, could be a couple things? Did it ever run right? Did you mess with anything or did it just start running crappy out of the blue. I would go over all vacuum lines and air intake tract, check for unplugged sensors (IAC, MAF, TPS, IAT), timing or firing order wrong somehow, PCV or little screen under PCV jammed up, spark plug wires all where they should be?