I have a few applications that absolutely refuse to install into anything but C:\Program Files or C:\Program Files(x86). Changing the registry keys for default install folders doesn't seem to provide any satisfaction and so now I'm wondering about throwing a NTFS junction in there to force these pesky applications to cooperate.

There are files currently in use within Windows so it's quite likely I am not going to be able to do this within the active OS. Is there some bootable Windows 7 system tools that would allow me to make this happen? Seems I will need the ability to copy files (with permissions!) from one drive to another, as well as make the junction for Windows.