Good article. It's a similar process to what I used whenever I had to peer review scientific papers for publication. The other recommendation I would add is "read slow, then read slow again. Then read slow yet again". It helps to catch things you would otherwise miss by reading it as you would read anything else. I've on more than one occasion in this way caught the authors saying something as fact that they had no references for, and after Googling (another good recommendation in the article), their stated fact, only to find no references to it anywhere. Reading slowly and carefully also helps you connect the dots in the paper's thesis.
Also watch for "the" versus "a" or "an". It often indicates a bias in the paper if it's not backed up with good references. For instance, "X is the major input to Y" vs "X is a major input to Y". For instance, the last paper I blind peer reviewed just before I left work, as part of their background, not their thesis, the authors claimed that copper from brake pads is THE number one source of copper pollution in the marine environment. They had no reference, so I hit Google, because it sounded a little fishy to me. While there were a few articles, mostly from legislators and environmental NGOs relating to bills and laws stating that brake pads were THE contributor, numerous other links, including actual technical papers, only indicated they were A major contributor, with a pretty big variance in percentage of copper input into the ocean. So while it is a major factor, there is no conclusive evidence that it is THE major factor. Sort of like "AGW is an input into climate change" vs "AGW is the major input into climate change". :)
