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If the heatsinks are hot, the thermal paste is working fine as the heat is moving from the chips to the heatsinks. They need more airflow.
The heatsinks are designed to take airflow from a top-down cooler, such as the stock one. Since your cooler is the "tower" style, you are getting little to no airflow over the motherboard. A well placed fan should take care of this.
Personally, I'd opt for a higher CFM exhaust fan. It's possible your heatsink fan is as fast or faster then your exhaust fan, leading to increased heat and lack of airflow under that stream of air between the two fans. A higher flowing exhaust fan should pull air not only from the heatsink but also from the area around it, including the MOSFET/NB cooler ...
Actually I favor more intake fans than exhaust but I've seen countless times when someone will get a really nice CPU heatsink moving 85 or more CFM then point that fan at an exhaust fan moving 50 CFM.You just gave me the answer to all my problems. I done countless remounts for my HSF and I stil idle at 38-40c on 1.250v on the cpu.... I still have my eye on the yate loon fans. So it's better to have more exhaust then intake? Cuz so far I have 2 intakes, 2 exhaust, and 1 slot open on the top for a 140mm or 120mm.