babs,
I think the order is strictly up to you and the activities that are important during your trip.

I'll be visiting CA with DH next month and we will fly into and out of SFO, but will go directly from the airport to Pacific Grove. We originally thought we'd do the Monterey Penisula mid-trip, but the logistics didn't make sense. See my thread "Northern CA trip".

We aren't trying to include Yosemite because fitting all the things we want to do into 6 nights is already a problem!

Too bad you can't go a little higher on your budget...Union Street Inn in Cow Hollow gets great reviews and includes breakfast. I don't know about parking.

Frankly, I think the biggest lodging question for you is Yosemite, not SF. At this point, it's doubtful you will be able to get anything except perhaps a tent cabin in the park itself - the hotel rooms sell out very quickly. I personally really dislike the tent cabins, mainly because they are so close together you really have no privacy, but if you're only there one night, maybe that's okay. But I would check on the availability of lodging right away. You may end up having to find a room outside of the park, and that can be a drag - it can take anywhere from 30 minutes to more than an hour to drive into the valley just from the park entrances, depending on the time of day and how bad the traffic back-up is.

When I went to Yosemite, we were not able to stay in the park. But the place we stayed was pretty nice and convenient. I'll try to look it up. Not that it's still there, but the area would work.

We are debating bidding on priceline for the fisherman's wharf area or doing one of these hotels:

Inn on Broadway
The Warkwick
The Columbus Motor Inn

If anyone has input on these specific hotels please let me know!!!