Could it be that a voltage to the motherboard is bad? It is a long shot, but if the lightening shorted some component that is pulling down that voltage, any circuit it powers will not work.
Can you check the voltages into the bluetooth board or out of a USB port?
Do you know if the USBs all send data to the same serial device on the motherboard? I do not know if Bluetooth also feeds the same ASIC. It might (it is a low data rate device).
You will probably need to swap the motherboard.