MrsK and I did a much smaller version of your road trip a few years ago, driving the old coast road from LA to SFO.
In SFO we stayed at the Union Street Inn, which is in the middle of Cow Hollow and has a stack of bars and restaurants in that area. It's an old fashioned three storey timber house, that has a different vibe to a hotel. There's also a parking station a couple of hundred metres away which had a discount deal for parking. We visited more than a few bars, including Rose's Italian, and the Balboa Bar & Cafe.
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While we were there, we bought a day pass for the public transport, which included the buses and trains, although you pay extra for the cable car. On the vintage tram route near the harbour, they have a range of trams/railcars from the 1930s, including one from Melbourne.
On the way from LA to SFO, we stayed in San Luis Obispo - which is a real foodie and wine centre, and also in Monterey. Three days is a good amount of time to take in the old road, as there are a lot of good places to pull up and have lunch, and just cruise along.
Looking forward to your trip report.