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Do you think I could make the following cupcakes into PBJ cupcakes? I'm thinking of not doing the ganache and just doing a little dollop of jelly in the middle before baking.

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Re: Bakers a Question
You could either do that, or to avoid the jelly potentially drying out during baking, use the cone method after baking.
http://bakingbites.com/2007/09/how-to-make-filled-cupcakes-step-by-step/
The Nifty Foodie
Life/Craft Blog
I think that if you put the jelly on before you bake it's going to sink into the batter and dry out/spread more than you might like. It works great on thumbprint cookies but that's because the dough is dense enough to keep it in place.
I would either do a filled center like Joeys suggested (although I personally like using a pastry bag and filling from the bottom before icing) or just do a dollop on top like Martha's PBJ cupcakes. FYI I don't love Martha's PB icing - the recipe you have will come out better although you may not need quite that much milk IMO. My DH is obsessed with all things PB and it's taken me forever to get the icing juuuuust right!