at very lease scan it (im talking about real time scanning, not just pulling codes) and look for KR and what your narrow band O2's are at right now. i wouldnt worry about much else. that will at least tell you if your setup is safe. tuned is another issue. i would call some dyno shops and ask them if they have any experience using HPtuners and ask if they have ever tuned a 3800.
if you are getting KR stop beating it until you get it tuned.