The floppy drive connector is pushing 5volts on 1 wire and 12 volts on the other... The fan connector is also pushing 5 volts though a PWM circut. What happens when you attach 2 different voltage circuts to each to each other in an unknown way?
I am supprised the whole board do not smoke.
At this point if the HD is not detected i guess you can try pluggin it into another sata channel or try another HD.
The HDD is probably fine. But the motherboard is quite possibly fried – but not necessarily. Make sure the floppy connector has been removed. Try a different SATA connector as suggested, especially if you can try a different controller or SATA2 vs. SATA3. If it won't work on any of them, I'd suspect the motherboard is gone. Can you get into the BIOS?