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As a follow up to Difference between 1PI effective action and Wilsonian effective action, where can I find pedagogical material that highlights the similarities and differences between the 1PI and Wilsonian effective action?

Are there any good articles that that have a good exposition on implications to non-renormalization theorems in SUSY and to anomalies/instantons in Yang-Mills theories, as well as implications to gauge-invariance of renormalization group equations for the parameters in the two effective actions?

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These two actions have very few things in common. The 1PI effective action gives an exact description of the physics of your field theory, whereas the Wilsonian effective action is a formal object that is not physical (in the sense that you cannot get much physics out of it, even though the presence of fixed points in the RG flow is, of course, a very important thing).

In fact, there is an object that can be seen as the interpolation between the 1PI effective action, and the Wilsonian, sometimes called the average effective action. You should have a look at the non-perturbative RG, or functional RG. Some people have used it to study SUSY, you may want to read that too.

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