This is one of my favorites, It also takes a bit of work.
1.- Create a file.txt
Windows Registry Editor Version 5.00
[-HKEY_CLASSES_ROOT\Directory\shell\runas]
[HKEY_CLASSES_ROOT\Directory\shell\runas]
@="ElevatedCMD"
"HasLUAShield"=""
[HKEY_CLASSES_ROOT\Directory\shell\runas\command]
@="cmd.exe /s /k pushd \"%V\""
[-HKEY_CLASSES_ROOT\Directory\Background\shell\runas]
[HKEY_CLASSES_ROOT\Directory\Background\shell\runas]
@="ElevatedCMD"
"HasLUAShield"=""
[HKEY_CLASSES_ROOT\Directory\Background\shell\runas\command]
@="cmd.exe /s /k pushd \"%V\""
[-HKEY_CLASSES_ROOT\Drive\shell\runas]
[HKEY_CLASSES_ROOT\Drive\shell\runas]
@="ElevatedCMD"
"HasLUAShield"=""
[HKEY_CLASSES_ROOT\Drive\shell\runas\command]
@="cmd.exe /s /k pushd \"%V\""
[HKEY_CLASSES_ROOT\LibraryFolder\background\shell]
@="none"
[HKEY_CLASSES_ROOT\LibraryFolder\background\shell\runas]
@="ElevatedCMD"
"HasLUAShield"=""
[HKEY_CLASSES_ROOT\LibraryFolder\background\shell\runas\command]
@="cmd.exe /s /k pushd \"%V\""
2.- Rename the file.txt to file.reg
3.- Click in file.reg
It'll create a regular right click context menu for most if not all possible menus.
4.- Accept confirm authorization about it.
5.- Enjoiy it
Note: Change the text "ElevatedCMD" to whatever you want, this text will be displayed to execute the CMD, and if you added it and wants to change the text, only search in regedit, open it with Windows+R and type regedit and Enter, the regedit will open, search "ElevatedCMD" with ctrl+B(Finder) and F3(Next) and edit any concurrency.
Let me just get one thing out straight away, importing a huge registry file like you did is a bad idea.
When you export keys to a .reg file, you're simply creating a file that will contain instructions on how to re-create the keys you selected. Note that it will only take care of creating keys. Thus, when you later import the file, a merge will happen. Keys that don't exist in the registry any more will be re-created (which might be a horrible thing to happen) and keys that have changed will have their value overwritten (which might be just as horrible). Keys that were created from later boots of Windows will still exist after importing the .reg file.
A .reg file can even contain instructions to remove keys from the registry completely (although that won't be the case when exporting from the Registry Editor). So it is advisable to know exactly what a .reg file contains and what it will do. With a 480 MB file, it's very unlikely that you'll be able to know what will happen when you parse it.
At this point, I have serious doubts if you will be able to recover from this and get everything back to a proper working state. Luckily, the result of this doesn't seem too catastrophic. Good luck! If you have shadow copies enabled, the guide How to Restore Previous Versions of the Registry in Windows 7 might help.
I know that there are several guides online (like the one on the Windows website) that treat the .reg file export as a backup of the registry and, to some extent, it is. It represents a certain state of the registry at some point, but merging that state with a later state isn't really advisable (as you've just found out).
However, if I wanted to make a proper backup of the registry, I would copy the registry files from C:\Windows\System32\Config. Those could simply be replaced later to fully replace the state of the registry.
Best Answer
Had the same problem. Once you accept running under elevated permissions, the "root" of the elevated session does not have the same relative location for the actual command.
If you specify an absolute address for the file it should work.
Now the $.42 question... what is the current directory for the elevated session in which the command is running?