Much of Tool 5 pertains to pre-existing issues in the dataset(s) used for secondary research. You can use Tool 6 to describe limitations in your analysis due to usage of proxy variables (“Are any of your demographic variables (or a set of demographic variables) standing in as a proxy…”).
Use Tool 2 for describing how “soft” conflicts of interest (“Are any of these “soft” conflicts of interest applicable to your work?”) could influence or could appear to influence your findings.
Use Tool 7 to enumerate reasons why you may have been unable to engage in community consultation.