Ok. I spent about an hour yesterday just improving the airflow in my case, and I did not notice any change at all in temps. Before, the two front fans were being blocked by PSU cables, but now they are both open. All case fans are on 100% speed. My CPU is a Q9300, and the cooler is an Xigmatek HDT-S1283. I know that this is a good cooler, which is why I know that there is something else wrong. Not only that, but my temps are the same whether the case sides are on or off. I know that it has good airflow. I used the Thermal Paste that came with the Xigmatek because that was all that I had. It also was a real pain to install with the push pins and am also looking at getting an ACK-I7751 Retention Bracket just to make it easier to install. I might also get some AS5 which seems to be good. Well, enough of that...here is my results.
 
My results after 15 mins of idle with speedfan and realtemp, along with my Sensor Test results after idle.
 



 
And also my full load tests while running prime95 Small FFTs.
 

 
I ran the stock Intel Cooler for one day but didn't get to monitor the temps with it. But I am almost positive that it did better. I just need to know what's wrong and will try anything.

SO ur temps are 45 C idle and 56C load? Also are u at stock speeds? If your answers are yes then the cooler is not doing a very good job. I would recomend first changing the thermal paste. Make sure you get all of the old **** off with alcohol and then I would apply either OCZ thermal freeze or Artic silver Pro make sure it has solid contact between the CPu and HSF. If this doesnt help then I would suggest RMA the cooler. Hope it helps.

It doesn't seem to be running at stock speed according to screenshots, it seems to be running at less than stock.

Idk. I never changed anything. It is the stock speed and vcore.