The photos show two types of Japanese flying boats used in WWII> The 'Emily' seen directly at right has a tail cone gunners position completely different than that found at the "B-29" wreck site. However, the nose gun bears similarities. No little windows just behind it as are found on the wreckage however, and the shape appears to be different also.
Two other details about the H8K Emily of interest are that based on the 'possible identification' of a crashed version on a Saipan runway just after the US invasion (photo at upper right) it may be correct that there were 1 or more Emilys on Saipan. Also you will notice from the color photo (top left) and the bottom right photo that the propellor spinner does not appear to be the same as that found on the wreck.One other possible positive attribute is that the Emilys had a single nose cannon as does the wreckage (if the gunnery position found at the wreck site is indeed from the nose and not the tail). Some possibility but not a certain identification.
The other flying boat type shown is the H6K-3 "Mavis" (2 middle photos). The Mavis is also a 4 engine flying boat but has no similarity to the wreckage found at the muisnamed "B-29" dive site. Ruled out.
I have looked at quite a few other types and have not found an exact match yet. I'll keep searching. Meanwhile, if you have any information about this, please leave a comment and let me know.
I'll also be looking at some US planes in the theater at the time for a possible match. The remarkable thing about the wreck is that there is almost nothing left of the fuselage to identify it. There is not even enough wreckage around the site to have been a fuselage. Perhaps some of it was carted off in past times. As I said, if you have any info, please post it. Thanks.