I question the need for clearing the cmos since that has nothing to do with the actual problem. In order to see a direct short when going to plug the power in on a floppy drive you would have to had to force the plug on upside down since the plug slides onto four wire prongs.
Apparently you now smoked one entire rail since the 12v feed for each floppy plug is tied to a molex type plug used for an ide drive HD or optical. If that was the only rail you will have no choice but to replace the supply since sending it in for a new harness will end up costing about the same.