Why didn't you buy JFK-AKL if this is a concern?

As you may be aware, this was not a fare sale -- it was a fare error. There's a huge thread about it in the mileage run forum.

It's an urban myth that there's a magic button in UA's reservation system that "links" PNRs; this is completely false. When the agent mentioned "cross-referencing" she was right; they simply put a note in each PNR indicating that you are connecting on flight ### and the locator is ABC123. The idea here is that if the flight is boarding and you're not there, the gate agent may investigate your record and discover you're making a connection.

If you miss your initial SFO-SYD flight, you have two choices: (1) refund the ticket (this fare is fully refundable, IIRC) or (2) reprice and pay the difference, which will probably be about $5,000 add collect.

If I were you, I'd put up with an extra long layover in SFO so there is plenty of time for your JFK-SFO to get delayed.