So you have gotten it to the point that the neutral wire comes from the wall socket with no other wires and the .1 ohm is resistor hanging on the end of it with the primary of the transformer across the resistor? This sounds VERY suspicous to me. Are you sure you don't have a broken ground lead on your scope probe? Hook the scope across the secondary so it shows the noise and then short it out. You should never have a signal on a scope with the leads shorted.