Well, I was able to answer my own questions. For everyone else's benefit here it is:

(1) Even though the two of us shared a record locator, the PNR is stored by ticket number (makes sense). If I had simply not gotten on the first leg my entire ticket would have been canceled, but it would not have impacted the other person.

(2) I called VX and explained the situation. The first level phone person was quite knowledgable and understanding. She didn't quite understand why I cared at first and she started to quote me change fees and then realized the change fee was more than the entire ticket. That's when "it clicked" and she understood that I just wanted out of my first leg with no financial changes in either direction. She said that's super unusual but she could very likely get a manager to approve it as a one-time courtesy. That worked. Total call time was under 10 minutes and I never actually needed to talk to the manager myself. I got a new record locator and my wife's stayed the same. I was even able to keep my seat!