The U.S. can build trains and has a good rail system—for freight not passengers. It’s not obvious how Japan moves freight, but the U.S.’s rail system evolved to move freight efficiently. That is a huge difference and not necessarily the result of corruption or incompetence.
Maybe. Japan has plenty of freight by rail, but you can’t look at (say) the California high-speed rail debacle and blame that on cargo.
My understanding the rail share of freight is relatively low in Japan compared to many other developed countries. Most freight moves by truck or coastal shipping. Looking at a map of Japan, most of the cities are by the coast, so I guess coastal shipping makes a lot of sense.