1. old rail line positioning was also influenced by land ownership and existing human structures. and our know how how to deal with previously difficult geography has evolved. you may want to study "Stuttgart 21" or "gotthard rail tunnel" or Eurostar channel tunnel or Berlin Munich high speed track to get an intuition for what's possible if there is a political determination.
2. France and Japan have dedicated tracks. Germany has reliable high speed freight lines. again more than anything it's a matter of political will.
1. Geography and geology is tricky. Rail lines don't curve because the builders just love curves. There's geographic and geologic reasons for a lot of rail line positioning. That's in addition to people living/working/shopping in a place where it would be useful to lay track.
2. Freight lines own most of the track in the US. Amtrak gets to use those lines but freight has right-of-way. Amtrak must side track when a freight train is coming. Amtrak only has a few sections of the NEC as dedicated passenger track. Without dedicated passenger track Amtrak's schedules are all over the place. Freight trains have trouble all the time and passenger trains need to sit and wait while they fix/move the freight train.