FWIW: I've always been v. keen on making Amiga's out of PC hardware. Sadly though it's not developed any more I'd say Amithlon still remains the 'most authentic' route to a x86-based 'classic' Amiga...
...wonderful though WinUAE undoubtedly is the underlying OS will always prevent it from 'feeling' like an Amiga. Amithlon is a pig to set up with modern hardware but if you're selecting older components for the purpose it's not difficult at all.
X-Amiga's another option, though again sadly not actively developed.
ReactOS could make an interesting basis for such a project - especially as it's free. I wonder if it's mature enough? And if it would cause the same 'un-Amiga like' feel in the 'emulation layer'..?