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(not isolated in #2)
Connect the scope ground to your ground. Connect the probe to (1) which is 12V. Set the scope to display this in the center of the picture.
Now move the scope probe to (3) and you should see a picture where 0 volts across the transformer is the center of the picture.
Another way: We know there can not be DC across a coil or transformer. Set the scope to "AC" and the scope will remove the 12V DC from the picture.