Please clarify how long you actually have.You start out listing nights, then switch to days. Do you have 6 nights or 7 or 8?

The drive to Crater Lake is probably too long. Is Mendocino a must or just a stopover?
My thought would be to take the Amtrak Coast Starlight from Oakland on Sunday night (leaves about 9:30PM) north to Klamath Falls (arrives a little after 8AM). Rent a car in K-Falls and go to see Crater Lake and whatever else you wanted to see in southern Oregon and northern California (Redwood) in 3 maybe 4 days. Return the car in K-Falls and take the Coast Starlight from KFS to Portland. It is easy to get from downtown Portland out to PDX on the TriMet red line without a car.
The train fare may even be less than what the drop fee might be and would save a lot of driving.

Two alternative routes to suggest.

No. 1 - coast intensive. Map - https://goo.gl/maps/ENyaZufiQJtYvdXS6

Spend two nights in pretty Ferndale, CA, with the extra day spent doing the "Lost Coast loop." The Lost Coast is the last remaining coastal wilderness in California. The loop includes remote Mattole Beach and the Avenue of the Giants redwoods. Then drive north to Bandon, Oregon, for another two nights. Bandon has a nice "old town" waterfront with some good restaurants, but the real attraction is Bandon Beach and the beaches between the California state line and Bandon, such as Myers Creek or Pistol River. On the last day, travel to Portland via US 101 to Reedsport, OR Hwy 38 east along the lower Umpqua River to I-5, then I-5 north to the city. Look for Roosevelt elk south of OR 38 as you leave Reedsport.

This focuses on the redwoods and southern Oregon coast. Many lodgings require two night minimums, thus the nights in Ferndale and Bandon.

No. 2 - coast and Mt. Hood/Columbia Gorge. Map - https://goo.gl/maps/NS9jueHNrKDj81zK6

This bypasses the Lost Coast. Spend one night in the Eureka area (dinner at the fun Samoa Cookhouse) then two nights in Bandon, as above. Spend the last night in Hood River, having visited Mount Hood and the Hood River Valley en route. On the last day, travel to Portland through the Columbia River Gorge, stopping at various waterfalls and vista points as you do.

That's if I've got the number of nights straight.

My advice to everyone is to never ever pay in advance for a car rental whether one way or round trip. Too many things can happen to cancel a trip. If you paid with a credit card, you should be able to get most if not all of what you paid refunded.
I've taken the Coast Starlight both ways overnight many times between Klamath Falls and Sacramento. The coach seats are not really comfortable to sleep in but it can be done.

I lean toward Gardyloo's second route as I think Hood River ticks off the "scenic towns." And the Gorge is a great place to hike.

I also would consider Florence or Newport to be scenic towns.

Finally, if you think you will be going to San Francisco again sooner, you could do the redwoods later. Once you drop them from your route, you could go up I-5 and visit Crater Lake from Medford or Grants Pass.

After Crater Lake, go over to the Oregon Coast at Reedsport or Florence.

​​​​​​This works best if you visit the central Oregon Coast (or northern Oregon coast). There is a difference of opinion on this board. Some swear by the Southern Oregon Coast over the rest of the coastline.

Here's the deal with Redwood National Park. Due to political and industry resistance, it was designated as a federal national park long after the State of California had "cherry picked" some of the best groves as state parks. Of course it's terrific, but state parks such as Humboldt Redwoods SP, mainly south of Eureka and including much of the Avenue of the Giants, and Jedediah Smith Redwoods SP, located along US 199 north of Crescent City, have groves that are every bit as glorious as anything in Redwood National Park. Redwood National Park is sort of linear and a bit patchy, with "in-holdings" of private land in many locations. From the visitor viewpoint, it's nothing like the contiguous national parks (like Yosemite or Yellowstone) - you drive in and out of the national park often without knowing it, as you drive along US 101 and any side roads.

The Muir Woods are not a good comparison. While the individual trees are impressive, the extent of the forest in places like the Humboldt or Jed Smith redwoods is what leaves most people gobsmacked.

There's relatively little lodging within the redwoods; most is in communities on the fringes of the forest, like Ferndale, Eureka/Arcata, Trinidad and Crescent City, with a few places sprinkled in smaller communities like Klamath. That needn't spoil the experience; you can visit the Avenue of the Giants easily on the drive from the Bay Area to the Eureka/Humboldt Bay area, or the Jed Smith groves en route between northern California and the southern Oregon coastal communities. Park in one of the grove parking lots and walk off into the woods, and in no time you'll be surrounded by unearthly beauty. While of course there are hikes and trails in both the state and national parks, the redwoods can also be an "easy" visit - many of the best groves are very easily accessed, and you'll never have the crowds that you get in Muir Woods or down at the Julia Pfeiffer redwoods at Big Sur.

Crater Lake West Rim and access to it are open NOW. The East Rim is still closed, but you can see a lot. (Map is at bottom of my link, official national park site.)

Gardyloo is right--the redwoods are also great. And much more to see there than what you have done.

​​​I would probably choose Crater Lake, but this is your vacation, not mine.

https://www.nps.gov/crla/planyourvisit/maps.htm

San Francisco
Do you have reservations already? It can be expensive, really depending on your dates. We often stay in Marriott properties, never had a bad stay. Marriott Marquis bar has great views even if you don't stay there. We once stayed at the Courtyard at Larkspur Landing when we had the family and a vehicle to park.

Southern Oregon Coast
Wild Spring Guest Habitat--Port Orford (very south end of Oregon Coast). Consistently gets good writeups. Looks lovely.

Brookings--This AirBnB got very positive comments from another Fodorite who stayed there.
https://www.airbnb.com/rooms/2176986...oI30K9TKyDwNDr

Columbia River Gorge
Skamania Lodge is a favorite for us. We've stayed several times. Beautiful setting, great food, lovely outdoor hot tub under the stars. Just over the river. Definitely a great place to go for adult time.

Hood River has a lot of small B&Bs in the area. A few are on farms--Sakura Ridge came up when I searched today. Pretty sure this is one where friends held a reception. But it's been a long time so I'm not sure.
Some are not in the online travel agencies although that's been changing.

Cascade Locks--Best Western

Hood River--Holiday Inn Express

The Dalles -- R&R Guesthouse we just stayed here last year and really, a very nice place and excellent breakfast. The Dalles is not as cute and far more a working town but it was a fun change.

Portland
So if you're going to have a rental car until you check out at the airport--which really makes sense, my number one suggestion is Inn at Northrup Station. Free parking. It's right on the streetcar line, is fairly quiet at night but zips you right to a lot of great restaurants and downtown.

If you wanted something a little bit luxurious, you might check your dates and see how expensive the downtown hotels are. You'd have to pay parking but still could be worth doing.There's been so many new hotels and remodels going on, it's crazy. Here are some I'd look at:
Brand new or close to it: The Paramount, Dossier, and the Hi-Lo.
The Woodlark, Mark Spencer, are both really well located.
Of the classic hotels, the Sentinel had a complete overhaul and is supposed to be really nice inside.

Pearl District--Two brand new hotels there, a Hampton Inn and a Canopy by Hilton. This might be the nicest Hampton Inn I've ever spotted. I stopped in during a heatwave last summer and it's really pretty.

You'll see great reviews for Embassy Suites on this board, but in my opinion, that's not as great of an area at night anymore.