Thank you both for the suggestions! We're considering the Tijuana angle, but my girlfriend is job searching now so we'll need to wait a bit to see if she can get the extra time off work since it adds at least a full day. It might even be worth using my Alaska miles to fly from SF to San Diego.
Re. the baggage question, I was referring to the skiplagged route where we'd essentially skip out on the final flight, making the connection/layover the destination. My concern was with respect to overhead cabin space and the risk of getting our luggage checked. This probably isn't relevant anyhow since the San Diego-Tijuana plan seems a lot easier and more likely.
Thanks again for the help!