Apple Wireless (aluminium) Keyboard on Windows
I struggled with this exact problem for months, and eventually settled on uawks as the best solution. Yes, the fn stuff can sometimes get a little wonky, but it usually works.
I started out with scancode mapping, eventually wrote some AutoHotKey scripts along with Veil's dll to add in fn key support, and eventually discovered that uawks did everything my stuff did but with a nice little UI.
Uawks is just a UI on top of AutoHotKey scripts, so you can always go in and tweak the code to support your own brand of hotkeys. You can add in a little scancode mapping if you need to do something that uawks/AutoHotKey has issues with.
My final solution to the problem ended with me buying a Mac, so there's always that.
You can try the Microsoft Keyboard Layout Creator which should allow you to define the keyboard mappings.
EDIT: and this blog post might give you some tips on how to use it with an Apple keyboard
I had the same issue as you do and found out that installing Bootcamp on a plain PC will actually work. I've got the USB version of the same keyboard running with full fn compatibility for page up, down, home, end etc..
Of course you need to extract Bootcamp from the OSX install media, but there are guides just a Google search away.