South from Tecate or Mexicali
I will give you a couple of perspectives. A few years ago, my son rode from Calgary to Cabo San Lucas. He entered Mexico at Mexicali and took the "gulf route". Mexicali has a little hectic getting his bearings but nothing major as he headed south on MEX-5. It gets rural fairly quickly with little traffic. He continued on MEX-5 at the MEX-3 split where it got even more rural. He always found food/water but it was sometimes just the convenience store variety. However, he loved the mostly deserted beaches of Gulf of California. There was a few stretches of dirt/gravel/sand but that were in the process of paving it so I can't tell you how much is still unpaved. He connected with MEX-1 after quirky Coco's Corner (little food but a lot to drink) and continued south toward Cabo.
If you ride from San Diego toward Tecate, the US side from Otay Lakes Road to Tecate on CA-94 is hectic. We rode it from Tecate to San Diego so we had major downhills on a very twisty narrow road with heavy traffic. I can not recommend you ride it, especially east bound. Note I have almost 40 years and over 50k miles of touring so I am not just being wimpy. Maybe we hit it on a bad day (Tuesday mid-afternoon) but if I was not flying down at 35-40mph, I would not have enjoyed all the traffic whizzing by me. However, it was a scenic road.So if you go "inland" I would suggest you take ACA's Southern Tier route over to El Centro, CA, and head south from there.
However, if you want to head south from Tecate (maybe come in on ACA's Sierra Cascade's route), I would consider MEX-3 ok to ride. While I have not ridden MEX-3 south of Tecate, I have been doing a little research on and off the past view months and it seems to have a nice shoulder most of the route and even has a wine region near Guadalupe (NE of El Sauzal) and enough services.
Whichever you choose, have a great tour!