Tony,
I have been diving the site since the late 90's (I organized the trips for C and Gary along with a few other to dive it.). I have assisted in the production of shows for Discovery, History Channel, NHK, BBC, Monty Hall and a few others over the years along with helping research dives for Professor Kimura and recently got to do some work with Professor Schoch in the area. I have 100's of dives on the monuments and the surrounding areas to include the main ruins site, the stage, the stadium and some unnamed deeper sites. Most of the active study of the site has stopped after Professor Kimura retired and submitted his latest finding on the site. There will probably never be a definitive answer on the site due to its age and location (underwater) which has destroyed any absolute proof of man-modification of the structures. The uniqueness of the structure in the area leads one to believe in man modification but even if not modified by man it would have served as a gathering place or place of interest to ancient man. The dive itself is awesome, also the surrounding sea life of Yonaguni is worth the trip in itself.