I think it is bad, 56V which is going to be regulated down to 5V will probably result in overheating. Should be 14-15V or so.
I'm thinking the transformer, or wiring being connected to the wrong output voltage.
Also this 11.9V goes to the MPU, frying certain components.

Whatever you do, do not plug in extra boards with a voltage this high.
First check the transformer voltage and compare to the schematics like setzkor already advised.

No, I don't see how a voltage can be this high if not coming from the transformer. The AC secondary should be approx 14.2VAC. An unloaded transformer may be a bit higher, but nowhere near 56V.

What do all the other voltages read when J5 and J6 are connected?
Of course J5 and J6 have to be connected, since they are connected to the transformer.

I'm thinking a short in the wiring of the transformer. Perhaps some secondaries shorted with each other inside the transformer.
What do all the other secondaries measure? And compared to the 14VAC circuit.

And what does the transformer of your other machine read in the EBD?

There's really nothing else where the voltage can come from.
And your DMM reads correct, since the altek MPU failed to boot, and the other voltages are measured correctly.

What's the voltage on the MPU?
Perhaps the voltage regulator.