I know a lot of CC bakers use the WASC as the base for many of their other flavors of cakes, but I believe it's not the same when used for cupcakes based on how cupcakes bake.

Is there a great "base" recipe that works great with cupcakes?

Hm. That seems like an odd statement to me. I use the same base recipe (similar to WASC) for both cakes and cupcakes with no problems.