Hi Fodorites,
We're planning on driving from Houston, Texas to Guadalajara, Mexico and from there back towards San Diego. As of now, we're totally clueless as to which highways are preferable, what are good/safe places to stop on the way, and which border crossings will be best. My SO is somewhat worried about safety (on and off the road) as neither of us has driven to Mexico before. Any advice would help! TIA

You need to get Mexican insurance at the border. Try to NEVER drive at night. It has been awhile since we drove in Mexico. I do recall not getting the proper stamp at the border and us having to drive back & get it. We lost a lot of daylight time. Maybe someother fodorites can hel. This was when my kids were young maybe 20 years ago,
We have friends who drove down Baja last year with no problem-have fun-Chris

If you post your questions on www.zihuatanejo.net directing them to "Linda from Canada", "lee" & others they have traveled this route a number of times on the way to Zihua.

Just a few kilometers across the border, you'll have to stop at the inspection station to get the "Temporary Import Permit" for your car, you'll need a credit card for this. When you return, stop again, check into the same type of place to return the permit and let them remove the sticker from the windscreen. Since you're returning to San Diego, you'll be entering Baja California Norte, which is a Free state and doesn't require a car permit, the station will be somewhere close to the Sonora/Baja border.
Take the Toll (Cuota) roads, less traffic and also less COWS ! that's why the warning about driving at night. Plus the Cuota highways have emergency telephones on them and, I believe, your toll ticket gives you free emergency service.
One place I would suggest to visit is Zacatecas, a lovely city.

Obey all traffic laws! Even if you do obey the law you may be stopped anyway. We were stopped in the Yucatan last week, twice! We have been going there for years without an issue. We were not speeding but we had no choice but to pay the bribe. Driving at night is not a good idea and not just because of cows.