You can use the critiques to refute any of the studies that are listed by the pro-vaccine group, but it is also important to know that large population based epidemiological studies are not appropriate in finding causation in small sub-groups.
Here is what the Interagency Autism Coordinating Committee (IACC) said regarding the current research, "Numerous epidemiological studies have found no relationship between ASD and vaccines containing the mercury based preservative thimerosal." However, the Institute of Medicine report acknowledged, "limited in their ability to detect small susceptible subpopulations that could be more genetically vulnerable to environmental exposures." [here on page 127]
Additionally under careful review by independent doctors and scientists the epidemiological research not only is a blunt tool for determining causation the studies used have blatant conflicts of interest, poor designs and unsupported conclusions.
The studies used to refute the claim of vaccine autism causation are inadequate yet they are touted beyond the state of embarrassment. The good news is there is a title wave of research coming in that link vaccines to a myriad of chronic and debilitating childhood diseases. They are purposefully being marginalized to uphold a policy that hasn't even past basic safety analysis. You can review the 1000s of published works regarding the correlation of vaccines and a myriad of negative outcomes on my Validation page.