CPU Cooler: Stock cooler <-- This is your problem, trust me. Go pick up a Cooler master Hyper 212 evo (a very good bang for the buck cpu cooler). It should quiet it down a lot.

Try changing the fan speed in the bios, it could be pegged at 100% speed by default.

Welcome to the forums..It's probably the case fans and/or CPU cooler fan like Tucker said..You can hold the fans with your finger or something or momentarily unplug them to see which one(s) are noisey..The Chasis/CPU fanspeeds can be customized in the BIOS..You can do it EZ Mode, or Advanced Mode for more advanced fanspeed options using Q-Fan Control..Even Q-Fan is rather limited and software control using Fan Xpert (Included in AI Suite II) can reduce fan noise even more, and eliminate it altogether below a user-defined fanspeed curve with the Auto-Fan Stop option..The fans will run at 100% until the BIOS loads/beeps or until the OS loads AI Suite II..You don't have to install everything in the AI Suite II package, only what you need/want..You can get it here in the Utilities section if you need/want it..I suggest manually creating a restore point prior to installing AI Suite II..My fans would drive me bonkers without Fan Xpert.

Well, I used fan expert to get that percentange. I have fan expert set to silent mode for the CPU fan. But I can't just unplug the CPU fan, can I? I mean, even for five seconds, it would still get too hot, right?

Since you have Fan Xpert, the easiest way is to just switch the CPU Fan from Smart Mode to RPM Fix Mode and move the slider to 0 to shut it off/slow it down for testing purposes like I just did in the pic below..You can do that for any other fans too..It won't hurt at all to unplug it though, the CPU won't heat up all that fast. 
 

 
 

Update:
 
I found the cause of half the noise; a fan plugged directly into the PSU. Disconnected it. Still though, my system makes a little more noise than I would like it to. It is either the GPU, CPU, or PSU.
 

I am going to leave tomorrow morning, and be out of town for two weeks. I will try your suggestions when I get back. 

Is this forum dead?

So, I unplugged the intake fan, output fan, and CPU fan (with extreme caution to not let it get above 100F)
 
I then did lots off plugging in and removing fans.
 
I discovered that yes, the CPU fan is noisy.
 
 
However, after unplugging removing only the CPU fan, while quieter it is still a tad bit louder on idle than I'd like it to be. The front/rear fans are silent. That leave the PSU and GPU. It is a CX500, and I currently am pulling about 350W. So, I am pretty sure it is the GPU. However, since I have got an AMD CPU and no MB integrated graphics, and no spare graphics card lying around, I think I am stuck. I will however pickup a CMH212E on Black Friday, if it will fit in my case.

FX6300
Am I going to have to create a new thread?

I think you were given several possible answers to your problem. Starting another thread won't solve the problem. If anyone else thinks they can help, they will post here.