I've removed my EGR and affixed a block off plate, but can anyone tell me what they've used to plug the hose running from where the EGR used to be to the vacuum control solenoid? The engine is running rough right now and I'm wondering if plugging it at that point or further down the chain of connections would solve the problem. Thanks in advance for any help.

 

You need to remove the vacuum line from the nipple on the drivers side of the intake manifold, and block that nipple with a "vacuum cap".

http://shbox.com/1/opti_vacuum_conn.jpg

Since the EGR solenoid should only open during part load/cruise conditions - never at idle and never at WOT - its hard to see how it could cause the engine to run noticeably rougher, even if you didn't plug the line. Are you sure you got the blanking plates on, and sealed correctly to the intake manifold with a gasket or sensor-safe RTV?