Join Date: Sep 2005
Location: Hollister, CA
Bikes: Bianchi San Jose, Mercian King of Mercia
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Can't believe nobody's chimed in yet. I can't help you on all your questions, but a few thoughts occur. First, most of the route you've chosen will be quite busy, not just Hwy. 1 and Nicasio. Given where you're coming from, you'll probably find the roads to be wide and comfortable to ride on, however.
Camping is available at Point Reyes, but I'm not sure there are developed camping options between there and Petaluma, so somebody else may have some suggestions.
Hotsprings: Quite a few options -- all developed -- around Calistoga. Soaking in a warm pile of peat is all the rage there.
Berkeley to SF: The best (only) option is BART. Bay Area Rapid Transit runs in a tube under the bay. Bikes are allowed except during peak commute times.
Cool things to see: The area's scenic, no doubt. In the heart of the wine growing region, tourism is heavily skewed toward wine. Not to induce panic, but many, many of the drivers you encounter will be tasting their way from one vineyard to the next.
I find the cost of accommodations (not camping) in the area to be criminally punitive, if you've not already researched that. Restaurants tend to be expensive and crowded. The best seem to require reservations weeks in advance.
Expect July temperatures to be quite temperate near the coast and quite torrid in the heart of the wine-growing area.
I don't mean to dissuade you from your plans, but these are things I'd like to know were I planning a honeymoon. (We took ours over at your home base. I hope you enjoy ours as much.)