Man, I don't know how I missed that those were 0 byte files. So there is some progress, but mostly bad news I guess.
There is no backup of these extents so I did as suggested and made copies of other extents and renamed them, replacing the corrupt files. I could then mount the disk but can not open it. Using VMWare to mount I get an error "Z:\ is not accessible. The media is write protected." and can't view the contents. Mounting it using several other tools produces, essentially, the same error. This is definitely an improvement from before, where I was being told that the format wasn't recognized as a file system at all and it would ask me to simply format the volume on mount. Unfortunately I can't use vdk64 at work because we apply a GPO that blocks the local policy settings for accepting unsigned drivers. I'll have to wait until I get home to test.
As a second attempt, I copied the two extents (s005 & s008) from my golden image and replaced the corrupt files. In this case, s005 was actually quite large, some 300+MB. Sadly, the exact same result. I can now successfully mount the volume but can not gain entry. Interestingly, if I get properties on the volume it shows a 0 byte file system and no filesystem. Is this just a case where Windows can't read the fs?
Lastly, if I've skipped something important or messed something up, no worries as I'm working from a copy of the bad VM and can restore it back to it's original, busted state.