Did you do continuity test on a powered board, or on a board that had been recently powered. Voltage (or any residual voltage) present on the board when doing such a test will confuse the meter.
But I'm guessing that this is not the case and you do have a shorted supply on your PS3 motherboard. Finding such shorts can be a real head-scratch. But you have an advantage: you have done something to the PCB and then un-did that something, so it is that something that has caused the short, so obviously look at any work you've done.
Also fried chips can short the supply too and the source of your problem could be the flash devices.
Other than that, trying to describe how to fault find such problems via a forum is a problem in itself!