I just put a newer JDM 2.0 into an '01 Forester. It was similar to a 253, but no variable valve timing....
Anyway, yes. Best practice when swapping Subaru engines is to swap the intake manifold and wiring harness from the old motor. Obviously the EGR valve itself is mounted to the intake, so that takes care of that end.
My '01 Forester engine had a plug where the EGR pipe goes into the head, so I was able to just zip that out of the old engine (14mm allen, IIRC), and plug the hole in the new engine.
Moosens just had a thread on here with a Legacy with the opposite situation (non EGR engine in place of an EGR one), and he had to drill and tap the head for the port, so some engines do not have the plug there. In that thread I believe GD said it was an M20x1.5 thread, in which case an aftermarket drain plug would probably be easy enough to get.