The readings with a low resistance and then increasing, are caused by the bypass capacitors doing their job in reverse. When you first start taking a reading, current flows into the capacitors (because capacitors store charge) and the current flow looks like a low resistance to the ohmmeter. Eventually, it should level off and give you an actual reading of the resistance.
Was the 1-2 or 1-3 reading .5 M ohm up to 2 M ohm? Or "up to 2 ohm" as you wrote? If it only rises to 2 ohms, then there's definitely a short there somewhere, as 12V through 2 ohms would cause 6 amps to flow, which the power supply cannot supply. But if that was a typo, and it's really 2 M ohms, then no problem.
The 2-4 and 3-4 readings are fine. Most good motherboard I've checked show about 500 ohms of resistance, so .4 K ohms is right in the ball park. Even switched off, all the transistors have a little bit of leakage, and it adds up.