Technology

The problem is that Amtrak doesn't own most or even any of those rails, instead having to pay for the right to use them. The reason why this is a problem is that it's hard to upgrade rails to high speed when you don't own them. Amtrak trains also often have to stop and give passage to freight trains, which is unlike what you'd see in Japan where passenger trains are on their own, dedicated rails.

Flying is such a miserable experience from start to finish that I would opt for rail every time if it was viable, even if it took 3-4 times as long.

Even in Japan (basically the gold standard for public transportation) you are changing trains pretty regularly, have a LOT of stops along the way, and may need to do the last leg on a bus route that only runs twice a day.

In Europe it considered the worst PT. Bus once a day on a tiny island? Sounds insane. Japan still base their PT operation on schedules instead of intervals.

have a LOT of stops along the way, and may need to do the last leg on a bus route that only runs twice a day.

No... Even regular intercity train Moscow-Belgorod train makes about 5 stops in regional centers. High-speed like Sapsan(or a lot of similar trains) that stops only on last stop 650 km apart.