It's not that I have a fear of flying but it seems the best way to see Island countries is by island hopping and these three countries are all relatively close to one another if you take into account their most outlying inhabited islands.
I know there used to be a ferry between Taiwan and Japan that went out of business in 2008. And there seems to be no ferry between the Philippines and Taiwan either.
So how would a true adventurer do it? Can you pay fishing boats or the boats that presumably carry goods between these countries?
I should make it clear that I don't expect to be able to do it on one single boat. One from Philippines to Taiwan and another from Taiwan to Japan would also be good. (More changes would also be good.) I've also included the reverse journey in the question as I'd consider either way to be a great adventure.
Also at which points can I legally enter each country for customs and immigration purposes?
And would it be a lot more difficult to find a boat starting in Japan which I assume to be a much more strictly controlled country?
(Please don't answer "just fly it's easier", such answers will be off topic.)