I have bought a used intake manifold and it has an EGR delete plate on it. I've also noticed that the vacuum lines to the EGR are missing or broken. Is it worth my time hooking the EGR back up? If not, is there anything I need to do to ensure the car will run smoothly without it?

 

It may throw codes because it will not see the EGR sensor moving. I have the EGR blockoff plate that goes between the intake and EGR spacer. I hooked up the EGR vacuum and sensor wiring to fool the computer.
You can see the shiny plate in this picture.

 

check RMS INJECTION. they have a module that plugs into the harness to avoid the CEL. it will still throw one or two codes, but no dash light.