What causes the humming noise in my desktop?

Okay I have a Lenovo IdeaCentre K330B with an i3 Core Processor with 8 GB DDR Ram. Anyways, since I had the computer I have added a 2 GB Nvidia for X-Plane and purchased a new fan and heat sink to replace the factory, which was said to be better. I have ran some pretty taxing programs on it in Windows 7 like Adobe Master Suite and many others, until I decided to dump my OS and give 8.1 a try. (don't make the upgrade if you are comfortable with 7 because 8.1 isn't better). Anyways, I reloaded Office 2013, a few adobe programs that I actually use, and I run my simulator (un-simultaneously), and a few others. Now I understand hearing loud humming and fan noise when I run X-Plane or Photoshop, but the humming does not go away when I close all programs and let the system idle. It will pulsate hum all night driving me insane until I force my PC into sleep mode or power down. Anyways, what is causing my PC to run so hot? I ruled out a virus or spyware, and notice all CPU processes are normal. Is my PC just getting old or am I'm need of a more expensive cooling system. I can't stand it, it is so annoying. What can I do? Or have I exhausted all angles within financial reason?

The pulsating occurs because two of your fans are running at nearly the same speed:
http://en.wikipedia.org/...oustics%29

Have you installed drivers for your video card? Nvidia's control panel may offer some tools to better control the graphics card's fan speed, supposing your mod fan is using the same connector. (There's the possibility that the graphics card is trying to apply a fan speed that would make sense with the stock fan, but not with the mod fan.)

The Windows Power control panel's advanced settings has controls for the CPU fan speed. You might find options in BIOS to control other fans such as case/chassis or power supply.

There may be third-party applications that can give you finer control over your fans.

Your fan