ouch! You basically created a short circuit by doing that! Now with any luck, all you've taken out is the system fan header.
Both the fan header, and the Floppy connector are power outputs, and not the same wiring setup, so when you've plugged the floppy power into the fan header, it's probably shorted the 12V to ground.
FIRST RULE OF BUILDING A PC - Every connector on the PSU / Motherboard does NOT need to be connected
Let me repeat that - Every connector on the PSU / Motherboard does NOT need to be connected.
right on to what you can do next - you've probably toasted the system fan header - you can try a 3 pin fan on it, but it is doubtful it'll work. If it does, you are lucky.
The molex's you plugged together are fine - the two wire fan only needs the 12V power, thats why it only uses 2 connections - 12V and GND. the PSU molex has 4 wires for providing 12V (Yellow),GND (Black),GND (Black), 5V (red) - so the fan is only using the 12V and one GND for a complete 12V circuit. It was fine.
The mistake was the urge to plug EVERYTHING together - and you've basically killed the floppy connector. Does it have the 4 wires running up to the molex? And is the 12v (yellow lead) only burnt up to the molex connector? If so, I'd get snips, and just cut each of the 4 wires that go to the floppy connector - cut them right up beside the molex, being careful not to cut the cables between the molex and PSU. and make sure theres no exposed copper touching - use some electrical tape to cover the snipped wires INDIVIDUALLY.
If you do that, and it fires up (oops! not literally,no pun intended), you have been VERY lucky.
Worst case scenario could have been a fried board AND PSU.
Edited by latelesley - 6/11/13 at 9:21am