Copy files from one NTFS drive to another via a USB boot disk

Firstly, you can try to take ownership of the folder with windows itself. You must be an administrator for this to work! So, here goes.

1. Right-click on the folder and click on "Properties"
2. Go to the "Security" tab.
3. Click on the "Edit..." button
   1. Click on "Add..." and enter your username in the textbox
   2. Click on "Check Names", just to be on the safe side, and then click on "OK". Your account has appeared in the list of users.
   3. Click on your account and then select the necessary permissions (basically: select "Full control")
   4. Tada! That's done. You might have to repeat this process for other folders. If this doesn't work, please follow the next set of steps.
4. Instead of clicking on "Edit...", click on "Advanced" in the properties window.
   1. Click on "Change" next to "Owner:" at the top.
   2. Enter your username, click on "Check Names" and then on "OK".
   3. Select "Replace all child object permissions (...)" and click on "OK" again. And again... Tadah
5. If this also didn't work, click on "Add" instead of "Change" (step 4.1).
   1. Click on "Select a principal", enter your username, etc...
   2. Select "Full control".
   3. Select "This folder, subfolders and files" next to "Applies to:"
   4. Click on "OK", "OK", "OK"...
6. This is all you can do with Windows itself.

You might want to use a 3^rd-party program for some reason.

For this, please follow the instructions here: Add "Take Ownership" to Explorer Right-Click Menu in Win 7,8 or Vista - How-To Geek. After installing the mentioned tool, right-click on the folder and select "Take Ownership" as shown on the picture below:

Or you can use the program you mentioned yourself: Ownership Changer - Software created by our members - Neowin Forums

As a 'last resort', you can use a LiveCD of a Linux distro (Ubuntu, for example) to copy the files from the external HDD.

Or you can use GParted (yes, its main purpose is managing partitions, but as you can see here, (other) manipulation of hard drives is also possible)

^{btw, I assume you mean the "Users" folder? "Documents and Settings" isn't used anymore since Windows Vista. Well, nevermind, doesn matter.}

Have you tried ln.exe with "Smart Copy" function --copy?

Smart Copy basically creates a copy of the directory structure from the source location to the destination, but it preserves the inner hardlink structure and inner junction/symbolic link relations of the source, and recreates this inner hardlink structure and inner junction/symbolic link relation at the destination location

Smart Copy is a must if e.g. the whole content of a hard disk, which has lots of hardlinks/junctions/symbolic links, should be copied to another hard disk.