Check if ur CPU is overheating using temp monitor softwares.
The chances are after changing your motherboard, the thermal paste wear off. Check the paste in between the CPU and heat sink. Apply thermal paste if it is not sufficient or it is in very less amount. Laptop's CPU are designed such a way that if it does overheat or the heat does not flow through the heat sink, the CPU will work at reduce frequency and it will be slow.
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