You can leave everything hooked up as is, except to add a plate where the EGR hooks up to the inlet plenum. Then you will need a tune to delete the function of the EGR. That will be the only way to do it without it throwing a CE light.
Keep the vacuum lines hooked up. If you are going for more aftermarket stuff, then you can get it all without the EGR, but leave the EGR hooked up to vacuum with the block off plate installed. With a chip that should keep codes from coming up.