Just because it's dual core does not mean it must run much hotter. I am just starting out with an 89W 4400+ Ath64 x2 using a Zalman cooler and Arctic Silver in an Antec Sonata II case (has a duct to bring outside air to the Zalman Cooler for CPU). This is on an ASUS A8R32-MVP Deluxe mobo.
So far my idle CPU temp is about 36 to 38C, and running Memtest 86+ for an hour will bring it up to 40C max. It sounds to me like your CPU cooling is insufficient. For the temps you are seeing, the problem does not seem to be a minor tweak. Try these:
1. Check overall case cooling. Is mobo temp running high, too? That MIGHT indicate a case cooling problem. My case came with a 120mm fan in rear plus the PSU fans. I added an extra 120mm intake fan in front (behind the HDD's in this case design). My mobo temps run about 28 to 30C, (not heavily stressed yet - only Memtest so far) if I can believe the Hardware Monitor in my BIOS.
2. In upgrading, did you move any components / cables so that air flow in the case is severely impeded? Have you checked and cleaned the air intake filters?
3. Is CPU fan running at full speed? Or is it under some sort of controller that has it slowed down?
4. Maybe your CPU cooler mounting is not right and / or the thermal paste is not right. You can remove the CPU cooler (carefully - don't want to damage CPU!) then clean off the old paste and re-apply. Go to the Arctic Silver website for precise instructions on how to clean and apply.
5 In the forums, the best way to remove the CPU cooler seems to be: slack off the fan mounting mechanism (for the stock AMD system you just swing back the locking lever and unhook the arm ends), then GENTLY twist the fan maybe 10 to 20 degrees each way to break any sealing force between fan and CPU. If it won't twist DO NOT APPLY HIGH FORCE - you cannot risk damaging CPU pins - you would have to try another loosening method. Then lift the fan GENTLY. You should NOT have to pull hard. You want the CPU to stay locked into its socket. If necessary, try rolling the fan to one side slightly, rather than a straight-up pull. Once it's off, observe the amount and pattern of the old paste. For cleaning off, you probably can leave the CPU in its socket and use Q-Tips and iso-Propanol to clean it off gently. Just do NOT flood the area with cleaner that can run down into the socket! Alternative, of course, would be to release the ZIF locking lever and remove the CPU, but that means more handling of the expensive chip. Again, the Artic Silver website has good instructions for all this, even if you're not using their product.