The first thing to do then is dump the floppy drive since that is what is seeing an internal short there. Don't even try it again. Apparently that was your first mistake since the system ran normal without after the first attempt.
Besides dumping that you will want to start off with another supply in case any of the other wiring fused itself from the short. From there you can proceed to test each drive as you go along since a floppy drive isn't required unless you are starting the system by first booting off a 3 1/2". Those are cheap enough to replace anyways.
With a different supply in you can test the system there by first unplugging the optical drives along with the hard drvei to see if you get a normal post. After seeing that and shutting it off then try the hard drive to see if Windows loads up and no harm to that was seen. From there follow the same method for shutting it down and plugging the optical drive in to if that escaped any problems.
The first thing to do following the clearing of the cmos which was a waste of time is first setting time and date followed by the boot order. Make sure the hard drive is set as the first.