So after quite some silence (and a lot of business trips and other stuff, which kept me away from AROS), I'll post an update for you ;):
From time to time I found a few free minutes, so I could implement all the missing virtual filesystem pieces step by step.
Basically you need to catch all m68k filesystem packets and call the according functions on the guest system. Now AROS as a host is a special case, because the native host filesystem supports the same features as the guest filesystem. The WinUAE problem, that the underlying windows filesystem eventually supports no comments, does not exist on AROS. So the best solution would have been to remove this middle ware completely, but I'll postpone that for a later time.
Nevertheless, now it works. It even works fast enough, the filesystem tasks expects to run in a higher priority than the main uae task. Not only on AROS, even on Windows WinUAE raises the priority. Strange for someone, who is used to Unix schedulers only..
So now, what's next?
No idea ;). So back to the gui:
I implemented BS_AUTORADIOBUTTON controls, so that with Windows-native-looking calls to the Windows API the unmodified WinUAE code can interact with the native Zune GUI. Yeah, I know, sounds like gtk-mui. But as I hate gui logic coding and everybody would scream "I like the WinUAE gui more!" anyways, the WinUAE GUI it will be (just with Zune gadgets).
And finally, when you now select a CPU in the gui and start uae, the cpu is really set to the right model and your Amiga boots in the right configuration :-).