Using transformer with 3 28.5V secondary windings to supply 57VAC/80VDC

You just have to respect the max current of the transformer ! Tommy say metal core transformers can withstand a lot of overload, he's right, but I would think a toroidal one is not this type, and you could have magnetic saturation.

If you don't know your load current, just put a fuse to protect the output and you will see.

I was wrong with saturation. I'm used to small ferrite toroidal transformers wich are sensible to saturation, but your is surely iron core. Like Tommy said, the limit is the temperature.
And even with ferrite, it's only one magnetic circuit, so saturation would only appear when the total windings current exceed the maximum of the transformer.
We don't care of unbalanced current between windings.

Tommy advice is to overload it and check the temperature, I agree it works, put the right fuse after test on the output and then. Are you even sure you will overload it ? Maybe not !
I would although consider to change it because I think it's a small one (you don't say how many amps you have), and I have many unused transformers. Maybe you don't. Have a look around you, it's easy to find some...

Doing a power supply.. For me no, if you put the three in series you will have 90VAC, better to use directly 120VAC or 240VAC in this case.

But once again, I assume your transformer is a small one (300VA ?), it's not the same if it's a 2kVA one, but in this case you wouldn't need to worry for the third driver.

If you can measure the temperature of your transformer, put a load, and check the temperature. As Tommy said, that's the unique concern. So, until 60°C, you are fine. Insulation can go above, but I'm not sure what would be safe for the insulation. I think I drove motors until 80°C, maybe 100°C, without damage but it's not a good idea at all, you will heat the cabinet and can hurt someone if touching it.

The sticker may be gone... It although may be printed on the side.

They use SMD fuse because the stepper driver is usually a controlled current source, so impossible to have an overcurrent.

I think you blow the current sensing resistor. There is no current limiting resistor in today's stepper drivers.
In normal operation, it's impossible, the board will measure the current, and open the transistor when it reach the maximum.
Either the current sensing is dead, either the power stage is damaged, and can't stop the current (a damaged mosfet is always closed). It's more probably the power stage.