bunch of quick questions......

removing the EGR w/o letting the puter know that you did, can lead to some nice pinging.

Well, I believe you are referring to the thin plasticky, black/white tubes. They are vacuum tubes, and if those are the ones you mean, yes, not plugging them can make your car run like doo-doo. With the car running, stick the ends of the tubes by your ear, and if you can hear hissing, you need to plug it.
There are two coolant tubes running to the EGR plate, and they shouldn't throw codes if you remove them.