Recover data after hard drive failure

A couple of days ago, I tried getting an old server of mine up and running.  It was working initially, but after updating and rebooting the system a few times the system refused to boot, dying at GRUB Rescue. I put the hard drive in another Linux machine to see what was going on, and the system partition was displaying as unknown.  I ran "fsck" on the partition, which got it working again; however, now the "var" and "usr" folders are missing! I've tried various things to try and recover the data, including running "Check" and "Attempt Data Rescue" (which crashes) on GParted, fsck, testdisk, changing the superblock, creating and mounting an image using DD, and nothing seems to work.  Even worse is, the files I want to recover are not in the "lost+found". The partition type is ext3. The partition reports "5 GB" of data is in use; however, only around "2.8 GB" can be accessed. I've tried doing a PhotoRec on the hard drive, but it seems completely pointless, as any recovered files are unnamed, so it'd be impossible for me to recover anything in a sensible manner.