First, the OS X installation on the PC certainly is pirated. Every Macintosh computer ships with OS X installed. You may have paid for an upgrade to such an installation. You did not pay for, and Apple doesn't sell, an OS to run on third-party hardware. Apple would be within its rights to sue you for copyright infringement.
Your system is so heavily modified that, instead of trying to remove the modifications piecemeal, you should erase your boot volume, reinstall OS X, and then go through the initial setup process, importing only your user data and settings from backup — not applications or other files.
Back up all data to at least two different storage devices, if you haven't already done so. The backups can be made with Time Machine or with a mirroring tool such as Carbon Copy Cloner. Preferably both. You must be certain that you can restore everything to the state it's in now.
Boot into Recovery (command-R at startup), launch Disk Utility, and erase the startup volume with the default options.This operation will destroy all data on the volume, so you had be better be sure of your backups. Quit Disk Utility and install OS X. When you reboot, you'll be prompted to go through the initial setup process. That’s when you import the data from one of your backups. For details, see here:
Setting up a new Mac from an old one
Import only "Users" and "Settings" – not "Applications" or "Other files." Don't import the Guest account, if it was enabled on the old system. After that, run Software Update. If you still have the problem, take the machine to an Apple Store or other authorized service provider for hardware testing.
If the problem is resolved after the clean installation, reinstall your third-party software selectively. I can only give general guidelines. Self-contained applications that install into the Applications folder by drag-and-drop or download from the App Store are usually safe. Anything that comes packaged as an installer or that prompts for an administrator password is suspect, and you must test thoroughly after reinstalling each such item to make sure you haven't restored the problem. Never reinstall the hacks from the pirated OS X installation.
Before installing any software, ask yourself the question, "Am I sure I know how to uninstall it without having to start this process all over again?" If the answer is "no," stop.
Never install any third-party software unless you know how to uninstall it.