tt120, in response to your Qs:

(1) Book all 3 (you, wife, friend) on the same PNR; let it "gel" and call back later to split the PNR.....I've never had a problem;

(2) Your wife's companion tix will be eligible for upgrade based on your status. When the PNR is split, of course, your wife's friend is out of luck, unless she has status of her own;

(3) I don't think you can buy F tix and get 2 coach tix for $99+ each. My MC cert has been sent off, and I have only the BofA cert in front of me - but they're both similar. On front of BofA cert it says. "...Certificate valid for roundtrip, coach-class travel..." and on the back I interpret what it says to mean, "all pax must travel in the same (booked) class and itinerary (italics mine)..."