I am going to assume you are referring to the condenser fan motor since you are using a regular fan in place of it to keep the compressor cool. If you replaced the main board then you can pretty much count out voltage supply to the fan dropping out if when the fan stops the compressor is still running along with the evap fans this means the system is supplying voltage to the fans. These condenser motors are dc voltage they have winding in them that attach to an armature (this is on the inside of the fan housing of course), one of the windings could be bad inside so that when it heats up after running a while its separating contact from the commutator and so it quits running , to make a long story short, replace the motor and your fridge should be fine.
Refrigerator Condenser Fan
Part #: DA31-00146B
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