There is a fuse for the USB built into the motherboard and I would have thought it would have blown first. But if it had your PC would still have run but without the USB. Since its not starting I can only assume that either the entire motherboard has blown or the power supply.
I'll have to leave it for others to supply any testing ideas as personally I have no idea how to test the power supply and would myself try another power supply first.
If it was the plugging in of the hard drive that caused this then there is a good possability it would have blown the USB ports as well even assumming the board and CPU is ok. If so then you can buy a USB card for about £10-20 so thats not a total loss.
First thing, open the case, see if you can detect what has been burning and check all leads. It could be something as simple as a lead coming out but the smell of burning does obviously concern me.