Where do I start......
It's useless unless it goes coast to coast. Distance between LA and NY is around 2400 miles. Sealing all that....good luck.
If you were going to do it. Why not two narrow diameter tubes, instead of one huge honking one. Look at the SST and the Concorde. Narrow hull. That way, even if you could lower the atmosphere by an appreciable degree it wouldn't need to be a vacuum. Which brings me to my next point. Carrying atmosphere for the passengers.
And no one has built a maglev of any appreciable distance. I'd make it a highspeed corridor on a narrow lifting body and call it good. At least that isn't a pipe dream. No pun intended.

High speeds in tubes are best attained by very long trains of tiny frontal surface area vehicles not much larger than a single person. High speeds would mean that serving meals and bathroom breaks on a train would be unnecessary, thus no isles would be necessary. Stations would have very long boarding platforms into parking lots with cabs ready and waiting, pre-positioned. A break at a station for a meal would mean a stop of you and your aero-car. IV nourishment, catheters, and anesthesia could move masses of people more efficiently over interplanetary distances. Tickets would be purchased online so stations would no longer be needed. Having everyone lie down head to foot boarding the train would maximize speed and minimize supporting infrastructure. Small diameter pipes are easier to design than large ones. Similarly light weight bridges could be used instead of massive expensive structures. Yes we could do it, but why?

Even if it was the perfect ride, @ 4000mph, what would that break neck momentum do to the human body? Does this thing also generate its own gravitational field? If so, it belongs in a discoid aircraft in space, not a tunnel under the ground.

I would put my money on a normal-air-pressure solution, running along or above highways, electric powered, fully-automated, modular and regulated to allow for easy and flexible shuttle cargo and passenger traffic with thinner infrastructures and lighter vehicles.
Monster projects are nice to admire on paper but not very practical. The ROI on this thing will be horrible unless we're talking about a mid-Europe/mid-US to Beijing sort of investment, where there's tons (pun intended :) of cargo traffic.
PS. I work for a rail company ;)

Not to mention....what happens if the train loses cabin pressure? You gonna put everyone in a pressure suit to prevent the passengers from boiling in zero atmosphere?

Good balanced overview. They will never get the construction costs back: twin 50m bore tunnels over 1000's of kilometres? And keeping a vacuum in that volume? good luck to that.
So much wasted volume, why not go for more conventional train dimensions? it's not as if you're constrained in train-length. ET3 is too far the other way for my liking, too claustrophobic. And superconducting power distribution? maybe, but you won't get the energy back either from this project.

Would be nice to have more info on how they would generate the vacuum, and what quality would be required/maintained. Could a design be developed whereby high level vacuum on has to be maintained around & ahead of the train, easing off once the train has passed? Another thought, and possibly daft - but if you can't maintain a vacuum, how about increasing the air speed in the tube? If the tube was circular, could air speed be pushed up to 500mph+ to offset any drag at the same speed? Trains could enter & exit the main 'loop' via separate connectors so that the air speed wasn't an issue when stopping at the destination.

Look,to all the naysayers.. they don't HAVE to go 4000 MPH.. the point of the article, is the same as all the 'popular mechanics' magazines of the 1950's that asked "if we have the capability of 100 miles per gallon engines, why aren't we building them?" or are you too young to remember those issues.. Oh the pain of age...;-(

it would be far cheaper and easier to build spaceplanes that fly above the atmosphere.

Removing wind resistance takes away a huge constant loss, but the energy needed for acceleration to high speeds is not affected, and not trivial. Kinetic energy increases as the square of speed, so an earthquake or other surprise could turn the train into a big explosion. @JPAR - the total skin friction in a tube is far greater than that on a train, unless the trains are extremely close together.