I usually keep all my data off C:\ as much as possible, anyway. Never trust a Windows system drive.
As for plugins and where they come from: starting from v1.x, the plugins come from plugins.calibre-ebook.com, which scans and mirrors this site once an hour, according to Kovid. In any case, you do need to be able to read and write to \AppData\Local\Roaming to install plugins; I'm not sure if that's still true on Win8 however, but I don't see why it should change. And yeah, calibre does use the \Temp folder for writing file downloads before it assembles it into a book and puts it in the library.