The plan is coming together.
I reserved a car this morning from Hertz in South San Francisco. I'll pick it up on Tuesday morning, and drop it off the following Wednesday morning. Going with an Economy Car, using my AAA discount and a AAA coupon code, it's going to cost just $181 for the 8 days.
At that price, the cost of Parking for a day in SF shouldn't seem so bad, and more importantly, we'll also be able to save money by getting a hotel Tuesday night out around Fairfield, which should be quite a bit less than another night out by SFO. From the looks of things, the public transit system isn't all that cheap either, so I think having a car should work out reasonably well for just one day in SF.
So the plan now is to arrive Monday evening, and head to an airport hotel (nothing booked, yet, but will take recommendations if someone has a favorite).
Tuesday, get up, get the rental car, and head into the city itself. Plan right now is to visit Alcatraz, and then maybe enjoy some seafood around the Warf or head up to China Town, and then head to the Giants game. After the game, head across the Bay Bridge and onto a hotel.
Wednesday drive up to Crater Lake, Spend all day Thursday there, and then Friday-Tuesday making our way down the coast. Probably ending up at an airport hotel again on the Tuesday night, although that's not a must, since our flights don't leave until around 2pm on Wednesday.