Stops aren't that big a deal.
In fact, in the vast arctic, your stops won't be for passengers - but for crew.
Take a commuter train; a stop adds about 1 minute. You can compare the schedules of express and local commuters and that's about what it amounts to. In your case, you have a great deal more acceleration to do. But you climb through the first 130 kph even faster than a plain old commuter train, and get to 300 kph acceptably fast. Most of your accelerating is over 300 kph, but you're moving at a fine clip during that time, so it doesn't cost you that much time. The upshot is you can expect stopping proper to add 7 or 8 minutes IMO.
However, because of what I'm about to say, stops will be more of a "big production"; even with staff cueing people when to move, you won't have a 1-minute stop - it'll be more like 7-8 minutes of fussing and fiddling.
But have fewer of them.
Take a high speed overnight train from NYC to Chicago. That train is not going to stop at 125th St, Yankee Stadium, Yonkers, Hastings-on-Hudson, etc. It'll fly all those stations at speed, and make its first stop at Albany, the end of the short-haul regional district. If you're at Yonkers and want to ride it, you either backtrack to Grand Central, or you take the commuter to Croton-Harmon and change to the regional to Albany. There you change to the fast train, and your stops are:
- Albany (transit hub; end of short-haul service from NYC)
- Buffalo (big, end of intra-state service, transit hub for Ontario)
- Detroit (big; beginning of short-haul service to Chicago)
Note how we let the intra-state service in NY state and Michigan make it completely unnecessary to have intermediate stops. Someone going from Syracuse to Ann Arbor will simply board an Empire service to Buffalo, take the HSR to Detroit, and change to a Michigan service train to Ann Arbor. Connections will be timed, of course, and often "across-the-platform".
Your train will use that trick also. If you are in Paris, you must ride a TGV to Brussels to pick it up.
- (skip Minsk, they can't even get the Bug canal open.)
Now at this point, you're largely doubling the Trans-Siberian Railroad, and you'll expect that to handle all the local traffic. A Siberian customer might have to ride the TSR for a day to get to the station for this train. (though realistically your route would also accommodate more local/short-haul trains, reducing that to 6 hours for those people.)
Because an automated train in the middle of Siberia ain't gonna happen.
In fact, there's so little out there in Siberia, Alaska and British Columbia, that your main reason to stop will be crew change.
The simple fact is that it's not humanly possible to know 3000 miles of route. Amtrak has 800 km crew districts, and assuming your grade-separated route eases some of the knowledge load, let's say 1600 km. So 7-8 stops (depending on terrain) between Moscow and Hope BC. I chose Hope because terrain favors it, to use the word "favor" lightly. The last 7000 km have been rough terrain, hugging the Ring of Fire.
Terrain is not loving this plan
I know you want to go to San Francisco but the terrain will make you fight your way through tough mountains all the way down from Anchorage to the Golden Gate. You're better off swinging hundreds of miles inland, e.g. through middle Alaska, NWT, Edmonton, Fargo and on to Chicago, and avoiding the Rockies altogether.
In Asia, there's just no good answer. This has been looked at for awhile. I don't know Russia well enough to guess.
Crossovers and special work is not that big a deal, really.
It is possible to have higher speed special work. It's just more expensive. As far as taking up space, it doesn't need to be in a particular location; you can push it up the line a few kilometers and just have 2 tracks. Crossovers don't need to be a single package in the normal transit form-factor of an "X". They can be a simple switch onto a "branch line" which then rejoins the other side. Below it, grade separated, can be the other side of the X, allowing trains to swap tracks at speed without interference.
Special work right outside of places you're stopping anyway does not need to be fast. So the crossovers and yard throat coming into Moscow station, don't worry about it.
Only the regularly used special work out in the country needs to be fast. When trains are being crossed over for occasional maintenance, that can slow. Slowing isn't that expensive timewise; you get right back up to speed and it only sets you back a few minutes at your speeds.
Freight pays the bills
Strictly as a purely rational (non sci-fi fantasy consideration)... one of the gigantic mistakes that high-speed rail projects have made, and I'm thinking particularly of ones with huge engineering problems to solve... is to overlook freight. They think they're gonna make it on passengers? Get real, nobody makes it on passengers. The freight business doesn't work in Europe because it's too short-haul and suppressed by stupid regulations coughopenaccesscough. But America proves freight is ridiculously profitable in long-haul. They unload container ships in Long Beach, rail them to New York and reload for a sail to Europe, for profit, without government subsidy.
You'll probably want a plain-ole-rails freight railroad to shadow your line just for construction logistics. So plan to develop that into a serious thing that's ready to carry an endless parade of double-stack container trains at 120kph at the closest spacing possible. When you have frontier crossings like the Bering Strait, accommodate freight there too. The profits will offset much of your total cost.