A few things that might be worth mentioning
AFA_OS: If youre using emulation (ie. fast "68k amiga") I'd consider using this as it replaces the need for birdie, visual prefs, icon.library, not to mention it's a little more flexible than those 3 combined and allows a person to use Zune (which is more attractive), concurrently with MUI.
End results for both routes arent drastically different, but if youre looking for maximum eye candy potential AFA_OS is, in my opinion, a better option.
As for transparent menus, this is done with magic menu still, but needs higher than 8bit color, so youll need an rtg (gfx card) system.