About 540V DC unloaded is what I expected. This seems to point back to the rectifier. As I mentioned the original filter caps were only rated for 500V. If you have a variac, dial the line AC down enough to avoid pushing the filter caps over their voltage rating.
I believe we have concluded: With the tubes in, the AC from the PT is where it should be but the DC is too low. So the PT appears to be okay.
This may be harebrained: Are you sure the rectifier is wired correctly. AFAIK the output on 5AR4 is supposed to be take off pin 8 because the cathode is indirectly heated. If the wiring is reversed and the output is taken off pin 2 the voltage is being pulled through the heater windings.
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Not sure exactly what the result would, but perhaps it would produce the reported symptoms

.
Different tubes like 5U4GB have directly heated cathodes, so you can take the output off pin 2 or 8.
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5U4GB has a lot more sag.