It seems like your problems are with the external disk. I think you could try a simple trick to fool Windows: First, unplug your external disk, start your computer, turn it off, plug the external disk. Then change the letter of the disk. Go to Control Panel > Administrative Tools > Computer Management > Disk Management. Right click the disk icon, choose Change Drive Letter and Paths > Change > From the dropdown, choose a free letter.
This may fool Windows, but I wouldn't be too certain. If it doesn't work directly, try rebooting your computer. Some people have got their computer to function by unplugging it from the main power, keeping it out for a day... bingo, it started.
+1. Are you sure you ran the Take Ownership fully? It sometimes takes a while, even to start, and it may stop, just to continue.
YOU MAY WANT to take a look here:
File permissions in Windows 7 - "Take Ownership" reports success but I can't access my files
+2. Not a master in this art, but you could try right-clicking the disk icon > Share with > Advanced sharing > Advanced sharing > tick Share this folder > click Permissions > see that it says Everybody > tick Full control > click Apply and OK.
It's really a nasty problem, a lot of people are struggling with it. I did too but then, that was a torrent Windows 7. With the legal one I've had no problems. You do have a legitimate Windows? Not suggesting or suspecting, that's not the point.
As a Windows owner, you are entitled to their support. Some of it costs, some is free. But they are able to solve a vast amount of problems through Internet, and even via phone.
Best of luck.
I'll try to figure out more of this issue.