First: Please don't run any alignment tools without knowing exactly what's wrong.
Some might have noticed my recent superior strategy for light bulb replacement, which nearly bricked my computer. :D However, things seems somewhat stable now so I'd like to try and help you. I'm trying to get a clear picture of your situation and setup, and the more details the better so:
1. Is it a laptop or desktop?
2. What OS are you running? I'm assuming win7..?
3. How is your hard drive setup?
-Number of disks? One external (going bye bye), one internal?
-Size of the disks?
-Roughly how are they partitioned?
-NFTS partitions, right?
..from the info I read, so far my understanding is something like this:
*A desktop, running win7
*One external disk with data - most data rescued.
*One(?) internal disk - The system disk with least 2 partitions, C:\ works just fine, you can use the computer just fine. The problem is limited to a single partition, and you don't have any dependencies there. (Installed apps/games...)
*All partitions are NTFS
*This is the error you get:
http://win1337ist.files.wordpress.com/2011/03/whoa.jpg 5. Are there still 2 problems? I.e. You still have data from the failing external disk yet to backup, and your backup destination is have some form of corruption, or have you rescued everything from the external one to some other location?
6. Judging from the tools you've run it looks like there are no signs of physical damage on the internal disk, right?
7. You're currently running some data recovery tool, which is able understand the entire directory structure, and it is currently in progress of recovering data? To another disk or partition?
8. Is the situation taken care of by now, making my inquiry kind of pointless? ;)