When I placed the disk in another system I could mount it and look through the filesystem just fine. I even reduced the size of the main partition by one Gig using parted thinking maybe it would repair something that had been corrupted, but that was a no-go.
"/" had no files nor links to "initrd.img" or "vlinuz" , just the usual folders. I'm writing down the targets of those links now because I have a hunch I may have been able to just create those missing links and been good to go, I have no idea what those two files/links are though.
I was able to put another disk in this system, get a Live CD to boot into a usable enviroment, transfer files/logs, unmount the primary drive and allow a fresh install to use the entire drive. I'm putting everything together on the fresh system now.
It was the strangest thing, one minute I was using the Adobe AIR SDK from the commandline to package an AIR file on my Desktop, the next minute I'm getting errors telling me files don't exist, like I'd accidently run something like "rm -r *".
I looked through the logs, here's the last part of bash_history.
cd ../
cd hello-world/
../../bin/adloWorld.air HelloWorld-app.xml HelloWorld.html AIRAliases.js
../../bin/adl HelloWorld.air HelloWorld-app.xml HelloWorld.html AIRAliases.js
../../bin/adt -package -storetype pkcs12 -keystore mr.joebert.pfx HelloWorld.air HelloWorld-app.xml HelloWorld.html AIRAliases.js
sudo shutdown -r 0
cd /
ls
- cd ../
- cd hello-world/
- ../../bin/adloWorld.air HelloWorld-app.xml HelloWorld.html AIRAliases.js
- ../../bin/adl HelloWorld.air HelloWorld-app.xml HelloWorld.html AIRAliases.js
- ../../bin/adt -package -storetype pkcs12 -keystore mr.joebert.pfx HelloWorld.air HelloWorld-app.xml HelloWorld.html AIRAliases.js
- sudo shutdown -r 0
- cd /
- ls
That last ../../bin/adt/... was when it just didn't respond and I tried to look at the system monitor, then I kept getting non-existant file errors, even when I tried to restart from the menu, which is when I tried to restart via bash and got the error again so I tried to look in "/" and it didn't exist.
I still had a desktop and menus.
I
had a syslog that didn't appear to have anything special in it with the exception of the last line being something about an "execl" function or something. Apparently it got overwritten while I was moving disks around though because the log entries have todays date.

In any event I have a usable system again and the only thing I've lost is time and part of my mind. Hell the cookies to log in to Ozzu for my Opera profile were still good just now heh.
I think it's time to invest in an external HDD considering a TB drive is roughly $100 and would be more than enough for me.
I can deal with reinstlling programs as I need them once in awhile since I tend to be lazy and don't uninstall stuff very often, but jumping through hoops to save my important files is getting old. It doesn't matter what OS I use, it's a pretty safe bet that I'm going to have something like this happen once in a blue moon no matter what.
Strong with this one, the sudo is.