|No, system restore is not a small 2KB shortcut. It has (by your own definition) got to hold 9G worth of information.|
You don't seem to be tackling this the right way. "Search" only tells you about what MS thinks you need to know (a mere fraction of reality).
You need to show "hidden files" and also "protected operating system files". The settings are made in Control Panel > Folder Options > View. Among other things a grayed out looking folder will then appear on the root of C, called "System Volume Information". This is what contains your restore data.
I realise that system restore and the paging file probably only account for some 11G but it's a start.
Similarly, Registry Mechanic is a "program" and even just the unpacked download is way larger than 14KB, so this must also be a shortcut and not the program itself. If you are somehow mixing up little shortcuts with actual programs then you are going to be wildly out. Have you looked, for example, at the sizes of c:\windows and its sub-folders, also c:\program files?
My general feeling is that your disk usage is likely to be all accounted for somewhere if you look in the right places, rather than this obscure idea of the system misreporting usage. Did you ever go through the procedure I tried on my machine (2nd para of my #10)?
What you need to do to free up space is uninstall any programs that are unnecessary. Almost all "programs" are likely to have been installed on the C drive (including Windows itself). Only videos, pictures and other data files are usually stored secondary HD's.
It is good to "show all file extensions" and "hidden files". It is not so good to permanently show "protected operating system files" because all sorts of odd-ball files can pop up all over the place (even sometimes on the desktop). In your case you need to "temporarily" show the latter while you check out the sizes - but don't delete anything.
What's the time?