From San Francisco
, I would do either Klamath Falls
if you want to stay inland, or Crescent City
if you want to drive along the coast.
Assuming you have the extra time since you're staying overnight and driving over 2 days, those will be more interesting stops than just staying on I-5, which is the fastest route but the least fun.
In Klamath Falls, maybe try Maverick Motel
or Golden West Motel
, both are budget hotels that have clean rooms.
In Crescent City, you could do a campground or lodge, or look at Pacific Inn