I'm also not an expert in the field, but I am very interested in this topic and reviewing the available evidence to create a cohesive and easy to understand proof.
Some of the things the article in the OP mention indicates where he is getting his information. The "CDC whistleblower" allegations he refers to have been thoroughly refuted.
"(a) written by a lead author who also was lead author on another study which his own collaborator says was improperly manipulated to hide a vaccine-autism connection. Do they really need to rely on him as their sole source for arguing vaccines don’t cause autism?"
I didn't read that ridiculously long distraction you linked, did you? However every phrase in my statement I believe to be true. Thompson was a collaborator. Thomson issued a statement through his lawyer saying as follows: "My name is William Thompson. I am a Senior Scientist with the Centers for Disease Control and Prevention, where I have worked since 1998. I regret that my coauthors and I omitted statistically significant information in our 2004 article published in the journal Pediatrics. The omitted data suggested that African American males who ...
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.