MSBuild error “CSC : error CS2001: Source File ‘x’ could not be found” with Linked Files after upgrading to Visual Studio 2012

Try getting the Build Logs,

http://msdn.microsoft.com/en-us/library/vstudio/ms171470.aspx

it seems that csc task could not find the source file. One cause it you import the wrong file.
so you have to edit the project file via normal Text Editor.