I haven't read everything here but I think larkimm is generally correct. At some point you have to trust the agency and move on. If the agency changes its mind later then runners should no longer use it.
From what I have read, the whole NOP saga with Rupp boils down to the possible use of testosterone. All we have is the anecdotes and the same could be true of other runners.
The Fleshman story was interesting but other runners have asthma (Radcliffe, Geb) and WADA has given a view on thyroid.
The Goucher evidence had to do with thyroid. The other Magness stories were rebutted with no comeback from Magness.
Also, I am not sure that I understand the poster who is comparing Bekele, Haile, Mo and Rupps body fat. Is there any basis for that?
All in all, the NOP / Rupp issue seems focused on whether you think he took testosterone. Who knows? Maybe USADA wi turn up more but I think hey have looked at this for years and have built a profile.
The Radcliffe story from this year left me with unanswered questions but I think she can argue for privacy even if that was not her previous position.