Sounds fairly straightforward k8o, Now I have to install WinUAE on my Windows machine again!

Due to the fact that I have a .uaerc_ file in My Morphos/System:/Emulation/E-UAE and I also have configuration files in My Morphos/System:/Emulation/E-UAE/Conf, can I ask what configuration file(s) you changed as well as the changes you made to the configuration?