casey, I feel your pain! Depending on which airports will work for you and your dates of travel, the suggestion by nsx could be the best for you. If you have to look beyond the "shuttle" cities, or you hope to travel days or dates unlikely to be DING!-eligible, it may be much harder.

I hope your situation isn't like the the kind of trip planning I usually have to do, which goes something like this: find the lowest cost airfare (either RT or open jaw) for either of two primary origin cities to either of three primary destination cities on (or about) any of three pairs of dates. None of the cities involved are judged by WN to qualify for inclusion in the "modify search" box that you get with the CA and NE co-terminal cities. At least between the Bay Area and the LA area you get to use the modify search feature. (I realize those might not be all the options you are considering.)

Bear in mind that due to some quirks in how Southwest Shortcut works, the low fare calendar often cannot be relied upon for finding the "right answer." (Those quirks have been much less in evidence of late; perhaps those special fare codes that are only valid on non-stop flights have fallen out of favor. Also, it sounds like you might only need to look at routes where most or all the flights are non-stop, so the quirk may not be applicable in the first place.)

Once I have the answer for which city pairs and dates work best for the proposed trip, I can move on to step two: Repeat step one for a traveler's sister who will make the trip at the same time. She is coming from a different part of the country and could also choose from two origin airports...so I have to compare the total airfare for the two travelers. Also keep an eye on whether the selected flights unduly shift too large a portion of the combined airfare among the travelers.

Found the lowest combined cost? Now compare the arrival and departure times of the lowest cost flights; the travelers are sharing a rental car, and because the drive from the arrival airport is 1 to 3 hours each way, they need to arrive and depart "close enough" to the same time.

Step three: remember that rental car costs could be vastly different at the different cities. Investigate whether an unusually high rental car cost in the lowest airfare city (or one-way between open jaw cities) might drop the "winner" to second place.

If the overall best option found so far seems pricey, repeat steps 1 through 3 for one more secondary origin cities and/or one to three more secondary destination cities that could work. Or look at whether it would be better to use an award for any one, two, three, or four of the legs; if so, are award seats available? In other words, I get to repeat half to all of the searches done so far, switching from paid to award seat search type.

I also look at custom connections because, while it is a long shot, I might find a schedule that is better than what WN publishes, or at least one that doesn't require getting up at 3am for the flight home.

Finally, I have to consider booking with a legacy for one of the legs that may have especially bad timing or high cost. WN's lowest WGA fare on one of the involved routes is often 50% to 75% higher than the competition, and their schedule choices are few and usually pretty bad. (Or non-existent; lately it has been dropping off the published service list, returning, dropping off again. Oddly, some of the best schedules available have been custom connections during the time published service was on hiatus!) So now I can do more searches on some other travel site, but the more advanced features of the other sites means at least makes it much less onerous.

If the overall best option found so far seems OK, but not great, first decide whether to book it or wait; then repeat steps 1 to 3 one or more times per day for the next, oh, six to eight weeks, hoping for a better deal.

Lately I've been getting bags of WN peanuts that tell me to "Don't go nuts searching for low fares." Given the process outlined above, I'm still trying to decide exactly what the message there really is! My "quick check fare after award search" discovery and my bookmarkable Southwest Shortcut URLs are at least a couple steps back away from the "gone nuts" end of the spectrum.