You can use the (free) Windows Performance Toolkit from Windows 8 which does run also on Windows Vista and later. There you can turn on system wide profiling to see what was going on in all processes at once. No instrumentation necessary. Only one reboot is required to set an arcane registry key which is done by WPRUI.exe automatically.
With XPerf you could enable IO Init stack walking so that a call stack is taken for every IO which is started. The only issue is that the stacks will be broken for 64 bit processes which means that you will see only the first method above the BCL methods of your code because there is a Windows 7 bug in the stackwalking capabilities of the OS.
A workaround is to Ngen your assemblies or move to Server 2012 or switch to x86 for profiling to see deeper call stacks.
You will see all file IO and CPU activity even without any call stacks and the file names along how long the hard disc was used. That should give you good information which part of your app is causing the disc IO. From the partial call stacks you should be able to pinpoint your issue even without full stacks.
The tool will give you much more insight than any commercially available profiler at the expense that you need to learn how to use it. Since the call stacks do not end at your code or in user mode but in the kernel you can also determine if e.g. the virus scanner is causing significant IO delays. But you need to know how your processor does work. This toolset was originally aimed at kernel devs which explains why you see so many useless columns.
In the picture below you see file IO and CPU consumption stacked. When you select your high IO file in the disc IO graph it will highlight in the CPU consumption all related call stacks which were taken at the same time while the IO was active. This way you can diretly navigate from the IO to your potentially blocked threads.