Back when I flew the CNZ deal, I found NZ to be very accomodating with information and assistance. Just call them and get the UA PNR and then call UA and get your seat assignment changed to your preference. Considering the brevity of the SFO-LAX flight, I don't know that I'd go through the effort, but YMMV. Welcome to FT.

My experience on the CNZ deal with mixed confirmation numbers was that the systems didn't talk to each other. I had to call NZ to confirm my seat assignment in C for SYD-AKL after UA gave me the NZ PNR.