You can reduce the heat by turning down the pots on the x and y stepper drivers.
I can't seem to locate the page on the wiki but turning them counter clockwise turns down the voltage, clockwise turns up the voltage. You want them as low as works without skipping steps.
I wouldn't worry about the heat. Steppers do tend to get a bit hot but IIRC it's perfectly safe to run them up to about 80C or so. It might've even been higher than that but I'm not quite sure, someone else will have to verify. If you're still worried about it you could attach a few small heatsinks to it to help dissipate the heat or you could try turning down the drive current.
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