When are you expecting to go? Weather can play a major factor in deciding where to go and when in that rather broad area. In a general sense, winter closes out some of the high passes but can make for pleasant temperatures in the otherwise brutally hot desert areas.
How long are allowing for the trip? Are you planning on camping or staying in established lodging, like hotels, motels, etc.?
I'm doing the trip first half of September. Will be staying in regular hotels/motels.
Although there is a limit to what i can visit. Just wondering if there were anything a bit off the beaten track that is a bit quirkier. For example, I recently did Highway 61, and visited Charlie Patton's grave. Or any interesting places to stay, stayed in the Shack Inn in Clarksdale during that trip.
Well, you're covering a lot of ground there. You should have a great time. We get Indian summer through mid-October. I don't know how committed you are to those locations, but if you are willing to go north of Yosemite, Lake Tahoe is a world class destination with lots of recreational activities. The east side of the lake is good for sunsets, especially south of Sand Harbor. If you're willing to even farther north, Lassen Natl. Park is an uncrowded jewel with a totally different feel from Yosemite.
In Yosemite, I would do the Tioga Road drive across the park. If you have time, you can keep going east out of the park to visit Mono Lake and Bodie, the abandoned mining town. In Yosemite Valley, I would recommend the awesome Mist trail for spectacular scenery you will not forget:
I would also say you MUST do the drive to Glacier Point for the best panoramic view I have ever seen in any national park.
In San Francisco, you can get some nice views of the GG bridge from the Marin Headlands or down at Marshall's Beach in SF itself. For sunsets, you can get some shots from around the Cliff House/Sutro Baths and for some nice views of the skyline, you can head out to Pier 14:
If you want to see the giant sequoias without the crowds, you can also head down to Sequoia/Kings Canyon NP. Not as spectacular as Yosemite, but has great sequoia groves, lots of black bears and no crowds compared to Yosemite. The road to the Cedar Grove area is very scenic.
In Vegas, I've heard the Red Rock Canyon is cool, but I haven't gone there yet.
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"You can't be young forever, but you can always be immature" - Larry Andersen