Check transformer voltages across each matching wire pair, not to ground
When comparing a replacement System 11 transformer with a known good one, readings taken from each connector hole to the cabinet ground strap can differ a lot and look like a bad transformer. Put the meter (AC volts) across the two matching-colour wires of each secondary instead, using the schematic; general illumination is the yellow and yellow-white pair. Done this way, the two transformers in this case read almost the same.
The transformer primary is at line voltage. Keep hands clear of the primary side and the line filter when the game is plugged in, and check that frayed wires are repaired before power-up.
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Source: Pinball Repair help group!! (Facebook group)