Regarding reading the rail voltages, I'm guessing that you read the +12V and +5V rails from a Molex connector. Because the Molex connectors don't include the +3.3V orange wire you were not able to take a reading from the connector. But a SATA power connector does include this rail voltage. With the computer turned off you can take a sewing pin and carefully push it though the insulation and into the conductor. Connect the red (positive) probe to the pin and turn on the computer. You will need to make contact with the case for a ground. You should be able to read the +3.3V rail. Remove the pin after you have finished reading the voltage.
There is another way to read these rail voltages, but this is a little more involved.
You will need to turn off the computer and unplug the power cord either from the back of the PSU or from the wall receptacle.
Remove the side panel, touch the inside of the case to discharge any static-electricity.
You will need to disconnect the 24-pin PSU connector from the motherboard. There is a tab which needs to be pressed to release the connector so it can be pulled free from the motherboard.
When you press the power button to start the computer this shorts the two header pins which the two wires from the power switch connects to. This in turn sends a signal through the 24-pin connector via the Green wire, this initiates the start of the PSU. In order to use the Green wire to start the PSU you will need to place a wire jumper between the Green wire socket and any black wire socket. A paperclip or a piece of insulated wire can be used for this.
With the preparations made it is time to plug the PSU power cord back into the wall receptacle. When this is plugged in the PSU should start, the case fan should be spinning at this time. This fan will place a small load on the PSU which will ensure a more accurate voltage reading than without a load.
After making you readings unplug the PSU power cord, remove the jumper and reattach the 24-pin connector to the motherboard. Plug the PSU power cord back into the wall receptacle. You should be able to restart the computer using the power button.