If your old engine had egr, and the new one doesn't, you'll probably get a check engine light at some point. You can clear it out of the system completely with an sct x-cal tuner.
I'd use the flexfuel rails and injectors, especially if you ever want to run e-85. They also have a higher flow rating than standard fuel injectors, which can help avoid detonation if you're planning other breathing mods.