Macbook Air 2011 CPU Maxes Out then Overheats and Shuts Down...

I've been having this problem for a while now but have learned to deal with it with SMC Fan Control to basically keep my fans maxed out at all times. This is obviously not ideal.
The problem is that at any given time some small, random task in activity monitor shows CPU usage that is very high, often at least 50% CPU and other times as high as 120% It has happened with the tasks like dock, safari web content and virtually any other task you can imagine.
For example, I just tried emptying my recycling bin and it hung half way through then my computer shut down. What is going on here?
Details:
- Macbook Air mid-2011 running Mavericks
- Never have more than one app open at any given time, usually just Safari with about 5 tabs, max
- 3rd party applications running in background include Dropbox, Copy, Backblaze, Flux, Sophos anti virus, Jumpcut, Caffeine and that's it
If I'm doing something like a Time Machine backup, I have to disable Wifi, max out the fans and only then will the Macbook Air remain cool enough to complete the backup, otherwise the Time Machine process maxes out the CPU, overheats and shuts down. This happens with virtually everything now.
How can I start trouble shooting this problem? I've run the hardware and system repair checks with no results, done an SMC reset, etc.
This really seems like a software issue more than anything, like something related to the way tasks/processes are handled...any ideas anyone? This is such an annoying problem!

Do the problems also occur in "Safe Mode"?
Safe Mode or "Safe Boot" is a troubleshooting mode that bypasses all third party system extensions and loads only required system components. Read about it: Starting up in Safe Mode
You must disable FileVault before you can start your Mac in Safe Mode.
Starting your Mac in Safe Mode will take longer than usual, graphics will not render smoothly, audio is disabled on some Macs, and some programs (iTunes for example) may not work at all.
Merely starting your Mac in Safe Mode is not intended to resolve the problem, it's to observe its performance without certain additional components.
To end Safe Mode restart your Mac normally. Shutdown will take longer as well.

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