To prepare gluten-free Guinness Chocolate Cupcakes, substitute the all-purpose flour with a 1:1 gluten-free baking flour blend that contains xanthan gum or another suitable binding agent. Additionally, replace the Guinness Extra Stout with a certified gluten-free stout or use strong brewed coffee for a non-alcoholic alternative. Always ensure that all other ingredients, particularly the cocoa powder and flavorings, are labeled gluten-free to prevent cross-contamination.