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Data Deleted, what next?

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Posted 23 July 2013 - 06:54 PM

Here is the full story. Hope I got this in the correct forum.
            Some how my Paypal was breached and two things were purchased on ebay. I assumed this was due to some malware or virus I acquired. I noticed on the computer that I was unable to go to google or ebay and that Excel files would not open without giving some macro error.  I ran Malwarebytes and it found a bunch of things, I don't recall what and now the log files are corrupted and make no sense when I open the text file.  My files were still available and could access and open them as far as I looked as I was dealing with the other parts of this issue.  
The system is Windows XP Pro 64 bit and has a 1TB SATA drive with two partions, a 500GB SATA drive single partition, and an 160GB IDE drive single partion. OS is on the first partition of the 1TB drive.
           I installed Eset Nod32 and set it to run on all drives and left it over night. I woke up and it seems to have rebooted and now said BOOTMGR missing.  I ran bootcfg /list and it said there was no boot.ini. I did a bootcfg /rebuild to make a new one. That did not solve the issue.  I ran fixboot then ran fixmbr.  Once it had the new boot.ini I then got ntldr missing so I replaced that and then ntdetect.com when it said it was missing. Then it said Hal.dll was missing or corrupt. Replaced Hal.dll in both system32 and syswow64 and it still persists with missing Hal.dll.  
            But the biggest problem is that somehow between running the AV and doing the above all my files on the 500GB and second partition on the 1TB are gone along with what looks like only the My Documents files on the first partition but other folders in C:\ are still there, and mostly My Documents in the 160GB and perhaps other are gone.  These files appear gone in the recovery console in a PE that I used from Hirens Boot CD, and when putting the drives in another computer.
          At this point I am not as concerned with it booting, I can reformat if needed, I just need to get my data back.  I would be nice to know how to fix this issue by my data is of paramount importance. Having done any and all of the above procedures on different computers over the years I have never had any drive show it as completely blank or show missing file from particular locations.  Nor have I had any virus do anything of this sort.
         How or what caused my data to get lost? More importantly how do I get it back as I hope that it is not truly gone.  Is it a MBR issue, a partition table, virus or what would cause this and how to fix it?
Any help you can give to help resolve this issue is greatly appreciated.

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