It's not really worth reading. I skimmed most of it. Most of the stuff has no chance of happening in our lifetime unless there is some other magical source of funding. The only things that have a shot are the projects with some other sort of funding (Metro North, Amtrak/Federal Gov't, Port Authority, etc.). Other than that, the freight railroads will have to pay for their own projects that they view as necessary. They have money.
I think it may be possible that NJ Transit might not be the perfect, infallible organization that most people assume it is.