Ah so you're familiar with the "S" code 3.4! Most of the parts are the same similar, from what I understand they had different heads and a slightly different intake and different injectors etc. That engine is "better" with a little more HP but a good chunk extra torque (200 ft-lbs?).
Hope all goes well and the car is not too bad off. EA is a solid engine but an EJ might be a slightly exciting upgrade.