Hmmm. I never thought of doing that. I don't worry about accidental grounds. I'm just really careful and I breadboard before I install the parts in a case. That way, I KNOW I am installing good parts.
But talk about coincidences: I just happen to have a bread boarded DS3P on my worktable plugged into my KVM switch.
So, after unplugging the PSU, using my handy-dandy Rat Shack dmm with range switch set to OHMS with the black lead on a black (ground) PSU pin:
orange wire (3.3 volts) to ground - about 350 ohms
red wire (5 volts) to ground - open
purple wire (5 volt SB) - about 300 ohms
green wire ( -12 volts) - open
yellow wire (12 volts) to ground - about 350 ohms for an instant, the jumping to open. Using KOHM range - about a thousand ohms.
In your case, with the system in a case, unplug all the PSU cables. Ground black (negative) probe to case. Red probe to all the motherboard PSU pins. The gound pins (where PSU black wires go) should read a short to ground. Everything else should read a few hundred ohms or higher.
If you do not read a short on the pins where black wires go, chose a ground pin on the main motherboard power connector, put the black lead of dmm on it and measure everything else.
Remember, we are measuring solid state electronics here. Different dmm's use different voltages and currents to measure resistance. And unlike resistors, semiconductors will respond differently. If you measured anywhere from, oh, a hundred to a thousand ohms, you probably do not have a detectable power suppy short.
I do not know what else can be done with home test equipment. Keep in mind that motherboard PCB's are multilayer and if anything else is internally shorted, you probably cannot detect it.
Fans - the good fans have an arrow indicating direction of airflow somewhere on the outside of the shroud. If it doesn't, the side of the hub with the label generally indicates the output side.
"If not, what do I absolutely need wired to check system so far, " Everything except the hard drives. With CPU and HSF, RAM, and video card installed, the system should successfully POST - the single short beep.