I'd probably just back up all your files...then rebuild the PC to vanilla OS, get all the windows updates, get the latest drivers for GPU and Chipset and also get the latest BIOS update. Then one by one, put your apps back on and use a good couple of programms to protect your PC, I use bullguard and malware bytes that seem to work well for me and neither slow my machine down. Also check the device manager for any warning, and the standard windows event logs.
Other things to be aware of...is if you have an Intel Multi Core CPU, some of the cores may be parked....google it, there are utilities you can get to check the registry and if parked, unpark them.
Check all the ram cards and other bits and bobs are all seated properly too....and check the BIOS, some do have a monitoring tab for CPU temps etc...
If still beeping after all this....then it will be a hardware fault....