The alternators are notoriously bad on the V6. So did you fix the EGR problem? I don't know about your model year, but the 2000's had a "recall" on the EGR being stock or clogged. It's not a safety recall where they invite you to get it fixed, but rather that they have a service bulletin to look out for this possible potential problem.

And also, does the sound get louder as you press on the gas? Describe more symptoms and how you get the noise.