I have got the Windows code signing working so that now when you install on Windows 8 you get a 'nice' User Account Control message as follows:
This is surprisingly fiddly to set up because you need a 'real life' identity confirmed with the certificate issuing company and then have to fiddle around with an acronym soup of different private key/ public key/ certificate files.
Also, thanks to a tip from petersvp on github, I have got the installer to automatically elevate and install with administrator rights. This should get rid of the problems with permissions on installing to the Program Files (x86) directory.
edit: improved icon