I can probably examine the papers cited in the above link in greater detail after work. On the university network now, downloading papers into dropbox, will look later.
I will note, without looking at ANYTHING yet, that one thing I quite often see in almost all non-professional reading of scientific biological literature is the latching onto one contextual or partial finding and yanking it across contexts where it does not belong.
Vaccination is probably one of the hardest topics to have a rational discussion about. I have some reason to believe that the author of http://whyarethingsthisway.com/2014/10/23/the-cdc-and-cargo-cult-science/ is someone interested in looking for the truth, not winning a side - at the very least, I'd like to help him when he says this:
I'm getting started on reading the actual papers, but I'm hoping this finds someone who's already done the work and wants to go post it on his site, or if not, someone else who's interested in looking through papers with me - I do better at this kind of work with social support.