Error 1 File 'Windows.props' not found. Visual Studio 2013 Premium

I'm getting the error Error 1 File 'Windows.props' not found. every time I try to build a JS Store app (Windows, Windows Phone or Universal).

I've been getting this error ever since i installed the 'Windows Phone 8.1 Emulator', I have tried restoring my PC to a previous state (a day before the installation), repairing multiple times, removing the Emulator, re-installing Visual Studio and I have also tried building on a different user account.

According to a few sources on the internet the windows.props file should be located in the following directory.

C:\Program Files (x86)\Windows Phone Kits\8.1\References\CommonConfiguration\Neutral\

Its not located in that directory. But I did locate the Windows.props file in the following directory.

C:\Program Files (x86)\Windows Phone Kits\8.1\DesignTime\CommonConfiguration\Neutral\

There is a Stackoverflow question similar to this but I couldn't find an answer that helped me.

Here is the information contained in my registry

HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Microsoft SDKs\WindowsPhone\v8.1\Install Path was set to C:\Program Files (x86)\Microsoft SDKs\Windows Phone\v8.1\

and

HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Microsoft SDKs\WindowsPhoneApp\v8.1\Install Path was set to C:\Program Files (x86)\Microsoft SDKs\WindowsPhoneApp\v8.1\

The complete error is

C:\Program Files (x86)\MSBuild\Microsoft\VisualStudio\v12.0\AppxPackage\Microsoft.AppXPackage.Tar‌​gets(561,9): error APPX1639: File 'Windows.props' not found. See go.microsoft.com/fwlink/… for more information