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the flight Tokyo -> Taipe starts at 400US
Taipe - > Seoul at 260 US
and Seoul - > Tokyo at 330 US
There was a ferry from Japan to Taiwan (going through Okinawa) but its no longer operating.
There is a ticket called the "Korea- Japan through ticket" wich includes the KTX Train from Seoul to Busan, the beetle ferry ride to Fukuoka and the train ride to Tokyo. This takes a long time and is not so easy to book. Its usually only worth if your destination is on Kyushu or your doing a round trip from Korea.
The Problem is that 2 off your flights are from/to Japan, and Japan is a expensive destination. Otherwise flights around Asia are usually cheap. If you use Bangkok or Singapur as a hub you can get nearly anywhere cheap. Return from Seoul to BKK start at 300US, and since Jetstar started the Jetstarasia you can even fly to Australia for not much money.
Good luck finding the right way for your journey.