Almost 24 hours with no reply, so I think I'll have a stab at this even though it has been a while since I have upgraded a companion on AS. IIRC, the rules for the MVPG also apply to the companion in regards the fare class so if your companion is booked in Y,B,M or H s/he would be available for an immediate upgrade if U space is available. If not, s/he would be placed on the waitlist BUT the one thing I'm unsure of is if they would clear before an MVP or after.

As far as being on a different PNR I know the MVP desk can somehow link yours with your companion and it should not be an issue at checkin since the waitlist from reservations is now carried over to the airport. I wouldn't think there would be a problem with one person being your companion outbound and the other on the return as long as you are only extending the companion benefit to only one person in each direction. If there is a problem since both are accompanying you each way I would suggest listing the same person as your companion for both flights and then just do a seat swap on the return flight.