I did the trip from San Juans to San Francisco in Oct 2007 followed by SF to southern CA in Nov.
Definitely do the trip in good weather. If you haven't, sign up for the pro level of www.bouyweather.com
so you can get a week's forecast.
Plan out your fuel stops and potentially stop for fuel whenever you can since the weather can cause crossing the bar of certain harbors to be treacherous or even be closed. For us, this was the key part of the planning since I didn't want to travel overnight (just the two of us) and we would trade-off fuel consumption for speed/time-to-arrival.
For my trip south, I was generally between 5-10 nm off shore. I didn't follow a fathom line, rather, I looked to minimize distance. For me, at that time, the sea conditions didn't seem to make much difference. We passed a number of sailboats, trawlers, motoryachts and fishing boats that were generally out the same distance.
Timing your departure with the slack tide is helpful, especially at the slower speeds, but I found the wind and resulting wind chop to be the consideration.
Consider the tides as well for coming into a marina. Some of the marinas can be very shallow (or the channel becomes very narrow) at low, low tide. Don't ask me how I know!
Finally, it goes without saying, make sure your boat is good condition. Have extra fuel filters. The weather was great for most of our trip, but just south of Coos Bay, OR we had 35+ kn winds and 15 ft confused seas for a couple of hours. Knowing that your boat is well prepared will give you peace of mind.
It is a long and generally boring trip, but I would easily do it again!