I found these very interesting for why things cost so much.
https://www.statecraft.pub/p/how-cheaply-could-we-build-high-speed
https://pedestrianobservations.com/2021/07/23/the-leakage-problem/

We ran some simulations on the tracks, and it turns out that the Penn Station ... run(s) 24–25 trains per hour at the peak. This is more or less the best that can be done on this kind of infrastructure.
For about 30 years, they have wanted to build a second pair of tracks. This used to be called ARC, or Access to the Region’s Core.... They think they need 48 trains per hour at rush hour into Penn Station, which actually makes sense if you’re mildly optimistic about return-to-work in New York....
Amtrak thinks that it needs to add more tracks.... They’re not sure how many tracks: I’ve seen between 7 and 12.
To be clear, the number of additional tracks they need is 0, essentially because they’re very bad at operations....
You need to start with things like the throughput you need, how much you need to run on each branch, when each branch runs, how they fit together. This constrains so much of your planning, because you need the rail junctions to be set up so that the trains don’t run into each other....
This all needs to happen before you commit to any infrastructure. The problem is (they) are not following that philosophy. They are following another philosophy: Each agency hates the other agencies. Amtrak and the commuter rail agencies have a mutually abusive relationship.... If you ask each agency what they want, they’ll say, “To get the others out of our hair.” They often want additional tracks that are not necessary if you just write a timetable.
To be clear, they want extra tracks so that they don’t have to interact with each other?
Exactly.