Been wanting to jump into this for awhile. Just catching up...
Let me add a few observation of my own to the mix.
Since 2006, I have made quite a study of that Tour and Stage 17 in particular. I grabbed every magazine, book, etc that came about it. I have a lot resources.
In the lead up to the final hearing, I do remember Floyd saying, with a degree of puzzlement, "Yeah, there's something else going on here." He knew that the facts weren't adding up.
He's often written off as "The hick from horse-and-buggy land" but I always paid attention when Lim and Ventura would talk about how "smart" Floyd was. His wife said, when asked about his future after cycling, "Floyd is so smart, he could do anything he put his mind to." Sure that's his wife speaking, but it only reinforces what others had stated. He's no dummy. He did his homework on the doping issue and he knows what is what. And his lengthy first-hand experience should weigh heavily on his acquired expertise.
The betting aspect to all this is interesting too. I remember when I first read that Eddy Merckx had placed money of Floyd to win the Tour,
after his collapse on Stage 16. Alarm bells went off in my head. The specifics of that story have changed a bit over time, but it was just an angle I hadn't considered up that point. Not implicating Eddy, it just opened up a whole other avenue. American sports have a rich history of mafia involvement. It blows my mind how little was made of the revelation that an NBA ref was busted and admitted to fixing basketball games! These things had been suspected for years by coaches and players alike, but coaches are fined and reprimaned if they even speak out about the refs during a press conference. The guy gets convicted, goes on 60 Minutes, lays the whole thing out, talks about complicity among many other refs, and...league officials brush him off as one bad apple. Sound familiar? At the heart of it was the mafia and mounting gambling debts.
http://www.cbsnews.com/stories/2009/12/03/60minutes/main5880547.shtml
Back to the 2006 Tour:
On Stage 17 team strategies were thrown into chaos. And much of the peloton was decimated. Many team leaders were out of the race by that point due to injury or sickness. Vande Velde said that they couldn't chase because so many of them were hurting and ill. He himself was puking throughout the stage, he reported.
But this is interesting.
Johan told his guys to expect an attack by Floyd. He knew Floyd's tenacity and he called it right. So it very likely that others in that circle would've known that as well. If they wanted set him up, they knew he'd be, at the very least, riding aggressively that day.
Now, he gets to the finish line and he's jacked. He's exuding anger and is aggressive towards those around him. Phil L. would later claim "that to me is a sign that he had very high levels of testosterone."

Although he completely switched to believing Floyd later on. But maybe he was carrying a bit of extra "T" even if unknowingly.
My last point in this long ramble...
Floyd and his legal team may have made a crucial error in judgement. By going all "wiki-defense" they showed too much of their hand. It seems they had the lab dead-to-rights in terms of sloppy procedure, etc. The lab was even admonished for it during the hearing. It was only
after Floyd's team starting leaking their tactics that the powers-that-be announced they would apply the carbon-isotope test, which eventually turned up supposed signs of synthetic "T" (in seven
other samples I think it was?) But that was not part of their initial accusation.
I have always wondered if Floyd's team had kept quiet on their strategy, and then gone to the hearing with guns blazin' on the lab protocols, they may have actually pulled it off. Remember, the more complex synthetic "T" claims were not part of the initial accusations.
It then became a giant chess match, with each side upping the ante. But it may have all started with something quite a bit simpler. One flagged sample that they thought would do the deed. They didn't count on Floyd's tenacity to continue the fight.