Traveling along the West Coast of the USA along U.S. 101 using public transportation

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For the first part of your journey, I'd suggest using the train. The Amtrak Cascades service runs between Vancouver and Eugene in Oregon:

Amtrack Cascades map from www.amtrakcascades.com/images/AmtrakCascadesMap.jpg

You can find their timetable on their website, but a few of the services are actually buses. I'd suggest trying for the train rather than the bus, as the views can be better!

You can save some money by booking in advance, but the fairly last minute tickets aren't too terribly priced, if you want to stay flexible with when and where you travel along the way

For the next part south, you could take the bus, or you could take the train. Amtrak run a daily service called the Coastal Starlight train, between Seattle and Los Angeles, which will get you from Oregon to Oakland (bus/BART from there to SF). Heading south, it does that section overnight though, which might not be so good for stopping off to see places. Booking for tomorrow for a seat is only about $75 from Eugene to Oakland, so not too bad for last-minute prices, but overnight in a seat might not be so much fun...

Alternately for that section, Rome2Rio offers some other options, including several Greyhound buses a day between Eugene and Sacramento. You could maybe look at using Greyhound to get you the next bit, with daytime travel and stop-offs as desired.

If you do take the bus to Sacramento, then there are frequent-ish Amtrak Capitol Corridor trains to get you to SF in about 3.5 hours for a fairly reasonable price.

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After some time with Google, I believe the answer is no. There is no problem going inland via Sacramento, either by bus or train. I don't know Greyhound's stop-off policy. I believe with advance notice, Amtrak allows one. There are a great number of fine tourist attractions on that route, but it isn't what the OP asked for.

Greyhound runs a service up 101 from San Francisco as far as Eureka and Arcata, but I don't see any way further North, even on county bus systems. Mendocino County has buses from Santa Rosa (connected to San Francisco by Golden Gate Transit bus service, fairly frequent) that will eventually get you to Fort Bragg on the coast or Willits on 101, but they don't seem to connect to anything beyond (except at Willits, you could get Greyhound to Arcata).

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