Files missing from external drive

Question

I have a 4 TB G-Tech RAID drive attached via FireWire 800. It was formerly a backup drive for photos/videos, moved up to a main drive when the old drive it was backing up failed. Problems got in the way of replacing it....
Anyway, all of a sudden, my files were gone. Just gone. For some reason, the folder hierarchy is still there--every folder, as best I can tell is where it was, but any and all data is gone.
Disk Utility found nothing wrong with the drive; DiskWarrior didn't, either. I booted from another external drive running 10.6.x, no change in what wa(sn't) there, and ran TechTool Pro 5 (I'm running 10.8.3 and don't have a newer version so it ran off the older OS); no help.
I ran Data Rescue for a few days and it seems to have recovered a lot of files--but we're talking almost 3 TB of data, and I shudder at how many months it's going to take me to get it back into a semblence of order, as well as how much I've actually recovered.
The part that makes me hit my forehead is that I ran the Deleted Files function, which scans free space only. I did so because, at the time I ran Data Rescue, there still was data on the drive, about 600 GB of photos/videos. But when it had finished, all THAT was gone, too, and I wonder if I should have done a Deep Scan and missed files as a result.
But here's the thing: If I do a Get Info on the drive, it says that the capacity is 4TB. But, if I open a Finder window and show the top level (with all of the volumes shown) and use List view, it shows  the drive as being 2.99 TB in size. So... is that data is still there, somehow? I.e., is there anything recoverable in a *useful* form--in the original folders and with the original names, rather than hundreds of thousands of undifferentiated files that DR presumebly found?
Side note, and perhaps a red herring. The drive had been running slowly for a while, though tests didn't show why; see here. The drive had seemed to recover itself, but then got slow again. I downloaded Drive Genius (demo) and tried to run the Benchmark function, only to find that it didn't run in eval mode. At some point, I found that my iMac was running slowly, and I opened Activity Monitor and found an odd process taking up a lot of CPU: dgse. Couldn't figure out what it was, and Googling didn't reveal anything. So, just in case I had a Trojan, I quit it. It was right after this that I found my data gone. I later tracked the process to Library>Application Support>Drive Genius
Sure seems darned coincidental....

Answer 1

Thanks. Ran it twice, but it didn't restore the files. Still, it gave me the following:
The original directory is damaged and it was necessary to scavenge the directory to find file and folder data.!
Some files that had been lost or thrown away may have been recovered.
Comparison of the original and replacement directories indicates that there will be no changes to the number or contents of files and folders. All files and folders were compared and a total of 807,104 comparison tests were performed.
• All errors in the directory structure such as tree depth, header node, map nodes, node size, node counts, node links, indexes and more have been repaired.
• Volume Information had to be scavenged from the file system journal.