If you were to get the EGR tuned out of your computer, could you simply block off the connection on the header and leave it at that? Or do you need to remove the EGR valve and the tubing and block those ports off too?

 

You would need to block off the tube going from the header, and also the back of the intake. You could leave the EGR itself on there since it would remain closed, but a block off plate would still be a good idea. Once it's tuned out you can remove all EGR components.

 

For the peace of mind to have a leak free intake you should block off the EGR ports on the intake.
If you want to just block off the exhaust gas port on the intake you will have to also block off the EGR port or leave the EGR valve in place. If you just block off the EGR port you do not have to block off the exhaust gas port.