A few years back, when a friend and I did the Baja, we got a San Diego friend to drive us to Tecate, so that we would miss the heavy traffic south of Tiajuana. When the secondary road (very nice) joined hw 1, close to Escondido, we then stayed on 1 most of the rest of the way. It was busy around LaPaz, but otherwise pretty good, from a traffic perspective. The final leg, into cabot, we left #1, and followed the coast route. Be prepared to ride on shoulderless roads most of the way. But if you can handle that, it is a great ride. Hopefully the traffic is not much more than we had it.
My favourite part was around Loreto.
We took a bus back to Tiajuana (24hrs), and the street car into San Diego. If you are prepared to ride #1 south of Tiajuana, but do not want to ride the San Diego section, you could take the street car to the border.