Hi;
As USB ports disconnecting, it can be an issue of the USB3.0 driver... But USB power staying on even after you shutdown is one of the motherboards features, not a fault, this means you can charge your USB devices (phone, kindle, tablet and etc) even if you turn of the computer itself, but if you're uncomfortable with it you can enable ErP in the BIOS to cut off the power to USB ports after shutdown.
There are more knowledgeable people than me here to assist you on your shutdown problem, but I believe it's because of a feature in windows 8 called fast boot, it basically hibernates the windows instead of actually shutting it down, and since the USB devices stay on after shutting down the system, one of your USB accessories goes crazy and sends a wake-up call to the computer turning it back on again.