I've been proactively rebooked by Air NZ onto QF because I was going to miss my connection in Syd due to NZ's delayed AKL departure and there weren't any other connecting flights until the following day. That was just Y though and I was rebooked into a flexible fare.
As previously discussed in some other thread, I'm a fan of jumping on the phone if I think there's going to be any potential problems to sort through my options. You can follow the ground experience but I figure there are more people on the end of a phone to be able to help than lining up for one or two agents. With organised transfers etc it would have seemed that things were going to work out.
I wonder if it's possible/easier to just fly Y (especially TT it's so short) then request the fare difference. Lose less money than buying a new J ticket.