Sorry for the late reply but things where a little bit hectic around here.
Thank you for the very useful information you gave us.
We will certainly take some of your tips into account.
the reason why we are goin through Kyushu from south to north is that we could not find a flight from Kagoshima to Iriomote, but we did find one from Fukuoka to Iriomote.
In the end it's not really a problem as we are not travelling by train but we fly from Osaka to Kagoshima.
The only train we will take is from Tokyo to Kyoto.
Again, thank you for the advice. It gives us a satisfying feeling that we planned our trip in a good way
Mike & Luve