Ansimp,
Wow, sounds like a great ride.
I am originally from California (3 yrs here near Portland, Ore) and spent many years riding/tramping around the Sierra including Summer work in Yosemite eons ago.
Although Yosemite always gets mixed reviews "breathtaking beauty!/horrid crowding! in the same sentence even, I believe oldwrench is correct, timing is everything. The Tamarack Crk campground (off of 120 just East of Crane Flat) sometimes has spaces available even on crazy crowded holiday weekends. Its true that the ride up to Glacier Pt is not to be missed, my advice would be to do it early in the morning.
I believe that gasoline isnt even sold in Yosemite Valley anymore so fill up elsewhere, Lee Vining for sure and maybe even a short ride later at Tuolumne Meadows because the gas station at Crane Flat will be crowded.
I like the Hetch Hetchy area, Middle Fork campground is hot and dry but less crowded than inside Yosemite Park proper.
After the bridge on Hwy 140 (Merced River/ El Portal area) was damaged a few years ago, Summer road work has delayed traffic so beware.
I just read that Cal Trans will probably be re-installing a stoplight on 120 between Buck Meadows and Cherry Lk turn off so be prepared for delay there too. Despite all of this news if you have never ridden 120 over Tioga Pass its well worth the trouble, just travel early if possible.
The other roads over the Sierra are amazing too, Sonora Pass/108 is really fun and The Dardenelles area is beautiful.
Ebbets/4 and Carson/88 supply plenty of great twisties and views as well.
I lived near Lassen Park for awhile, 44 and 89 are great motorcycle roads.
It does not look like your route takes you through/near Zion in Utah but man, oh man, is the Mt Carmel-Zion road a blast!
One October I rode out to Utah and the Mt Carmel road was so fantastic at one point I turned around and rode back some miles and did it again!
Summer of 2011 I encountered heavy smoke obstructing views near Crater Lake from prescribed burns, so you might want to check ahead for those Forest Service/National Park Service postings about burns they might be conducting. The Crater Lk and Diamond Lk area is still worth checking out even during burn season, Hah! the smoke helps keep that areas' legendary mosquitos at bay..a little anyway.
Sorry, I dont know much about Idaho, Interstate 84 East of Portland through the Columbia Gorge is magnificent, across the river in Washington hiway 14 climbs along the cliffs and has more twistys.
Good Luck and have fun!
Phil