Motors do run hot but not enough to trip the thermal cutout. The only thing I can think of is a lack of proper ventilation. However, the fact this is a new motor kills that idea. An overload will cause a motor to overheat but with a centrifugal pump with a properly sized motor, this should not cause an overload situation. On any motor a shorted winding would be a quick overheat and smoke, not a slowly developing problem.
How about more details on what you replaced with what? Anything else change between the motor swap?
Al
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