You should have an aftermarket CPU heatsink and fan, and at least 4 120mm case fans: 2 front intake, and 2 rear/top exhaust. Manage your cables to optimize your airflow: move the excess cables/wires to the bottom of the case, or between the back of the motherboard and the side of the case.
Like the post before, make sure you have enough fans for cooling. My current setup is a quad core with a beast of a motherboard and graphics card. I have 2 fans on the case and the CPU and GPU both have there own fans. The case has mesh at the front and lots of side inlets. I have found that this works perfectly even under stress but if you want to overclock, you may want more/better fans.
Particularly in your case, the fans may not actually be running at the speed whatever program you used says.
Also like the post above, tie some cables up to improve airflow.
That's great. If you moved it to a slot further away from the CPU, that would have helped the temps. But, we wouldn't have recommended that without knowing if you had another PCIex16 slot, and we did not know what motherboard you are using.