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I wouldn’t expect that the transformer is bad. It is normal for an unregulated power supply that the voltages be pulled down under load. Voltages lower than what is indicated on the schematic would imply that you have a short or some other similar fault on the board.
Do you have a bench power supply? If so, connecting the board to a bench supply is helpful for debugging.
A voltage sag from 40v to 5v seems to be more than a “sensitivity issue”. It sounds like a genuine fault and the protection circuitry is doing its job.