The waitlist/upgrade/flight pass interaction is indeed the problem. I generally have to get the SE desk to fix anything involving that combination. I still think if you get them to drop you from the "advance waitlist" you'll be able to select "upgrade" when you check in online (up to 24 hrs in advance) and it should put you on the "day of flight waitlist". But it might not work because it's a funny flight pass booking. I'd try it, and then if it doesn't work swing by YQR since it's so close.

Good luck!