If you have a clean extracted view then use probes to find the short (whether by name or by metal). You might also inspect for things like rogue contact / via / plain metal bits that have landed where they cause a short in fact. Zoom in to where you can see any bridging of stripe gaps and wander around with those probes lit up, and look for anything that is not all ortho and uniform width.
You could make selectable only the metalX/pin layers (if you used ploygon pins) and find any strays easily with ctrl-A (select all).
If you are convinced that the layout is clean, maybe removing all pins and hand placing the ones you really want, where you really want them, is the quickest and cleanest way out.