So, courtesy of involvement in Letsrun, shortly after Lagat's postive test and exoneration I was contracted to be an expert witness to the B sample testing by USADA after another positive A sample. So unlike 99.999% of posters here, I actually have experience with the entire process.
1) I'm not going into why Lagat's case was out of the ordinary and why anyone with a modicum of scientific education or desire to understand should realize that he was not guilty in the first place. This has been covered at length and the reasons shared. The A sample was egregiously mishandled, and the B sampel..while not perfectly handled...was handled better and negative.
2) After the Lagat fiasco, extra procedures were added to the protocol to verify the integrity and non-degraded nature of the samples.
3) Anyone who thinks Lagat's case was "fixed" does not have my first-hand experience. USADA was incredibly embarrassed by the whole affair. They were hostile to myself as an expert witness from the get-go. If I so much as spoke a word during the 3-day procedure, I would have been kicked out. I was told to hold my questions until the end, then the lab head was conveniently not there and I was told to submit my questions in writing. They never responded.
4) Standard lab protocol handling such samples requires them to be refrigerated during the entire processing of the sample. Their equipment was equipped with the capability to refrigerate (centrifuges etc) but they did not turn it on. Given that the reason for the error in Lagat's test was degradation, it made no sense not to simply turn on regrideration-capabe equipment being used. This made me understand how far we had to go in bringing protocols up to standard practice. Of course, I asked a question about this but like all the others they never responded.