The EGR is blocked off by a plate of aluminum and RTV sealant. The vacuum port for it is blocked off at the plenum. I had thought that it may have been the cause of my rough idle and when I went to get a new one all the parts stores needed to special order it. I didn't have time so I blocked it off.

There is no unplugged hose over the driver's side valve cover. There are only three hoses on that side. PCV, Brake booster, and AIR system hoses. All three are properly connected. Am I missing something?

The car runs pretty decent above idle as far as I can tell, but then again I am judgeing that against back when I had two bad fuel injectors, a bad fuel pump, and bad plugs and wires. There is still some hesitation sometimes, but I've encountered worse. It seems to rev up fine too, but then again I've never experienced it running "right".