This is a solved problem nowadays. Pretty much every pcb package produces 3D models you can plug into your existing CAD/CAM product design infrastructure.

3D is pretty solved, yes.

Pinouts... there is a reason we try to get all pinouts tested as early as possible, preferably on the first non-form-factor prototype spin if we can. In no event should key pinouts be first assigned or major changes made without a planned spin in the schedule following them....