When I received my gameshell, the slot on the conductive pads for the d-pad had a notch in the hole that it sits in. This only effected construction and not gameplay or usage of the unit. However, there is a load clicking noise that happens occasionally when doing quick direction changes on the d-pad.
I believe this is likely from a small bit of plastic still hanging onto the side of the dpad from where you snapped or clipped it off the plastic template. I suggest you try taking the dpad piece out and filing it down a tiny bit.