This has been an issue on the ZX12R almost since day one. The fix that Kawasaki did during the recall really did not fix the issue. The main thing you need to do is remove the connector going into the rectifier, and the connector leaving the rectifier and hard wire the wires together. Really the connectors are the biggest weak point. For whatever reason they cannot handle the current flowing through them. I removed the connectors and hard wired the wires, now everything works properly. The wires still get pretty warm, but not hot enough to do any damage.
Check out the sticky's on the top of the page when you click on this link. There is a lot of great info that will help you understand exactly what the issue is.
http://kawasakiworld.com/zx-12r/