What I've done since:
-Removed a scsi controller card that wasn't being used by anything (don't ask me I didn't build the machine).
-Booted into the recovery console, picked the boot drive, ran chkdsk /p restarted normally
-checked to see if the HD was set to master, it was
-went into the bios to see if it was recognizing the IDE drive, it was.
-Booted onto the XP disc and ran the repair, no resoltion
-checked to see if it was the hard drive or something else, put in a new HD and installed XP, and it boots.
-Put in the old drive again, and ran chkdsk /r. Still in process, after about an hour.
Think I am going to try and let it boot normally, and then run chkdsk /r again after that and again until it can't find any errors. I have gparted, as well that I can use.
I think my main worry is since it happened after running a windows update that I will have to reinstall fresh.