EGR Delete..
 

Just pick up a engine out of a NB and when assembling it I noticed the egr (tube?) was missing. I am talking about the tube that runs to the header from the intake. The valve has a block off plate on it and no hole for it on the JDM header (JDM motor). Can the hole on the intake run in open air? Or should I make a small block off plate for it?

It needs to be blocked off. Most kits come with two block off plates - one for the valve which it sounds like you have and one for the tube where it meets the intake.

Guess someone took it off before I got it.

The port in the intake manifold that the crossover tube connects to just goes directly to the EGR valve. The location on the intake manifold that the valve bolts to has two holes: one just goes to that port where the crossover tube connects, and the other one goes into the inside of the intake manifold. You can either: 1) leave the EGR valve bolted on but unplugged (it will stay closed), or 2) leave the EGR plugged in, but bolt on a blockoff plate that covers the two holes in the IM under where the EGR valve bolts up. If you run factory ECU and don't want error codes, then go with method 2. If you're running an aftermarket ECU, then do whatever.

JDM motors didn't get EGR valves, I can't remember for sure but I'm pretty sure the intake was never machined for the valve so that's actually a blind hole. I'll check my JDM intake later tonight.