Your other points are also valid, and more compelling, and the positive samples he submitted during evaluation of one of the tests are suspicous also. Still not conclusive due to the inability to verify chain of evidence, but that objection is so common from those accused of doping it has lost much credibility. For example:

I have been a big fan of Broncos linebacker D.J. Williams throughout his eight year career, but his current six game suspension is hard to criticize, even amid the same chain of custody objections; "substantiating" them by dropping the sample and kicking it into a team-only area undermine his credibility.

There is a preponderence of evidence against Armstrong, but not proof beyond reasonable doubt; which standard applies is up to the sports governing bodies.