Jonathan -
If you have the flexibility - then schedule your trip for the best possible window.
I might allocate 12 weeks - plenty of time - 3 extra days before and three days after.
If the ride goes a bit faster, I'm sure you can find something to do in San Francisco.
But having to crunch the last week or two of a big ride is a bummer.
Starting moderately is a good idea. 400 miles per week is not too much once you are in the groove.
Let's say you do 300 mi. each week, weeks 1 & 2 and 350 mi. each week, weeks 3 & 4.
That would be 600 mi. + 700 mi. + 3200 mi. = 4500 mi. Perfectly doable with flexibility.
It's also a good idea to start with a fixed route and deviate once you have the skills.
So, the first 1600 miles could be the Northern Tier to the Mississippi River.
I do not, especially, care for the ACA crossing of the Mississippi at Muscatine, Iowa.
The Mississippi is the mother river of the U.S. and has great meaning - the bridge is only so-so.
(The Rhine has similar meaning in Germany - but it is probably more like the Volga to Russia.)
That's why I suggest crossing at Rock Island on the Centennial Bridge.
The bridge is historic and visually stunning - plus, you have a long ride along the river before and after.
(Which is a pretty good trick considering the river runs north-south and you are riding east-west.)
https://www.crazyguyonabike.com/pics/docs/00/01/79/76/large/IMG_8159.JPG?v=0There are a number of good possible routes across Iowa - from Davenport to Sioux City.
Then, as I mentioned before, Hwy 12 to Butte and then US 20 to Chadron.
4500 miles gives you some miles to wander - and I would use them in the West.
From western Nebraska, you can head north into the Black Hills.
If you were to start May 1, it would only be mid June and ideal.
Then you could take in Devils Tower in east Wyoming before heading towards the Rockies.
The nice thing about riding Old Highway 16 from Clearmont to Buffalo is the mountain view.
You get 30+ miles of stunning mountains looming larger and larger - and snow-capped, too, in June.
Then you have a killer climb - but the rewards are the finest wildflower meadows in the world.
Nothing in Switzerland or Austria compares - not even Julie Andrews in "The Sound of Music".
Then you get a taste - just a small taste of high desert - before the Wapiti Valley leading to Yellowstone.
Yellowstone NP and Grand Teton NP are glorious - if you ride early, you can beat the traffic. Worth it.
The ride across eastern Idaho gives you another taste of high desert.
But then the Sawtooth Mountains and the long ride down the Payette River with hot springs is just "Wow!"
US 20 & US 395 in eastern Oregon is another and larger taste of high desert.
It will be hot in July, but not dangerously so as it would be in the Southwest deserts.
Also, services are more reasonably spaced - distances not so great.
Some lovely canyon riding along the Malheur River - then Lake Abert.
Lake Abert is an alkaline lake with 2500 foot (750 m) cliffs.
For a dramatic contrast, then head west to Crater Lake - a frigid, alpine caldera lake.
(Although the rim road should be open - there will still be lots of snow.)
Lake Abert and Crater Lake make an amazing contrast and epitomize the American West.
From there, you can finally head out to the Pacific Coast in northern California.
Here you can ride through the massive redwood forests in Redwoods NP.
Then there is the spectacular Highway 1 along the northern California coast.
Which allows you to end your trip crossing Golden Gate Bridge.
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East - 1600 mi.; Plains - 900 mi.; WY & ID - 1000 mi.; Oregon - 500 mi.; N. Calif. - 400 mi. - - 4400 mi.
Just a possibility. Google a few of the places - like Crater Lake.
Photo - Bighorn Mountains Meadow - - J