Well, you cannot directly “screw with the kernel” on Windows. I am not sure how that is keeping you from growing as a developer exactly though. You can write your own kernel from scratch using Windows as your host platform. And, of course, you can build a filesystem to use with Windows. You can even make it Open Source as well which many have.

If you do want to “screw” with the system on Windows, one option would be to replace the MS stuff one DLL at a time. You might take a DLL from ReactOS for example and make it work with your version of Windows, extending or altering it as you desire.