I've been researching Japanese origins and also Old Japanese texts and their various interpretations. I'm glad I found yourr blog. It seems like it's not very active, so I hope I can heelp with it :) And one of my significant shortcomings is my poor knowledge of Ryukyuan languages, so I'm really interested in the Ryukyuan data you provide.
As for the reconstruction of *b, *j(y), I completely agree with you. Linguists such as Vovin also cast doubt whether it is reasonable to treat *d as archaic rather than an innovation based on one sub-language (dialect, whatever). You have elaborated to show that /d/ that corresponds to Japanese /j/ is actually quite restricted. Possibly the /d/-/y/ correspondence was a convenient discovery for Altacists who could then compare "yo" with "dort" (four) "yama" with "dag" (mountain) etc in their science-fiction, which has been complete ripped apart by the likes of Georg and Vovin.
However, I still hold that the reconstruction of *p is accurate. The main reason is that the kanji for which /h/ sounds are pronounced in present day Japanese, /p/ sound or a similar bilabial is found in most Chinese dialects and also sinitic loans in Korean (some are transcribed as "b" but the p/b distinction is more of a aspirated/non-aspirated distinction rather than voice/voiceless distinction). I know there are some Kanji with /h/ that come from /f/ in Chinese, so perhaps there was a time when /p/ and /f/ coexisted in the Japanese phonological system.
I think that at the time of OJ writings the pronunciation might have already changed to /f/ or /ɸ/ but I think it is unlikely that it was never /p/ on PJ or OJ