It is rather helpful to find anything at all more about HIV - it is a confusing virus, and one that is certainly evolving along with our drug treatments for it. Research is stymied, sometimes, by the unwillingness of governements and funding bodies to confront the epidemic, based on, essentially, fear of talking about sex. More reasonably, it is also difficult to perform experiments with the virus, based on ethical and moral considerations with respect to possible test subjects....
(The moral of the story is, if you want a SARS flu vaccine, you get the Chinese government to make it....it have no qualms about injecting prisoners with `maybes.' In a Western country, one would never stand for such a violation of ones rights, and yet the West has no problem with using the results of such experiments. It is worthwile examining ones own moral view on these sorts of tests. )
You're right, there most certainly are those in the medical-historical community who argue that the precise disease may not have been yersinia pestis. The point is, there is no way to run a test on the DNA of a bacterium(or virus, if that's what it was) that was around 400 years ago. There have been inconclusive attempts to get samples from skeletal remains.
Note, from my previous post, I discussed influenza. Influenza mutates so rapidly, that even if an ancestor selected for CCR5-Delta32, modern influenza may do nothing of the sort.
Another intriguing genetic tidbit. It is widely believed that the black death selected for incidences of Downs' syndrome (which is an extra copy of chormosome 21) - witness relative population rates of Downs' syndrome vis a vis caucasian/European populations and other communities - there are significantly more individuals with the condition in caucasion/European populations.