Is it the master that originally had drum brakes, if so it probably has a residual valve built in and could be keeping the calipers partially engaged and causing the heat.You can pull the wheels and crack the bleeder valve and see if the pressure releases.
There are other things as well like internally collapsed hoses, master cylinder rod adjusted a little to long.
Are the fronts ok?
You will ruin the pads and rotors if you keep overheating them.
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