My first attempt was an utter failure in mold making which I documented here. I ended up taking the original polymer clay that I was going to cast and just baked it in order to attach it to the controller. It is heavier, clunkier, and not nearly as refined as I'd hoped, but at least I have a finished product and it actually works. The spine on the D-pad is a bit awkward when playing, but it's really more of a conversation piece than an everyday controller.
Filler and clear coat
Step 1: Take Apart the Controller
I left in the circuit board on the back half and did most of the work solely on the cover. I was trying to minimize the chance of breaking the thing before I even got my sculpt on.
Step 2: Sculpt
Once you have your sculpt, remove it from the controller face and bake it so it hardens. With sculpey, it's about 10 minutes at 275F.