Thanks for the report! You brought back memories of the Ishigaki/Iriomote/Taketomi trip I did in September 2001. It was great fun staying in cheap pensions/ minshuku and hanging out with fellow travelers and local residents. Ishigaki is rather grim near the port and airport, but it's beautiful once you get around to the other side, isn't it? There were very few tourists on Iriomote when I was there and I ended up booking a private day-long snorkel trip for some ridiculously cheap amount.... (Okinawan tourism was hurting pretty badly at the time as many Japanese nationals wanted to avoid being anywhere near a US base immediately post-9/11.)
Unfortunately, last I heard someone was putting up a big resort hotel on Iriomote right behind the pension where I stayed. Guess you can't stop "progress".