Yes, you can leave the EGR valve on and have no worries. it will not interfere with anything.
You can pick this up...
or do what I did with a piece of sheet metal..
Then before you ask the next question.....the cluster vacuum lines on the passenger side can be removed as well along with the solenoids they attach to on the back of the strut tower. The 2 lines that come off that go into the fenderwell can be left unblocked and just pushed into the fenderwell. Then you have the source line for it all that connected to the back of the intake. With what you are doing you will have it redone anyway... no need for the EGR vacuum.