Have you tried starting from a CD to see if you encounter these same problems? If, when started from a CD, you don't experience these problems, then it is definitely an issue with your hard drive and/or system.
If it is a system issue, try doing a clean install which would move your existing folder to a new folder called previous system. (this would require you to either reinstall all of your programs that use system extensions/control panels, or to "mine through" your previous system to find the appropriate extensions/control panels and preferences).
If it is a hard drive issue, then the best bet would be to back-up all of your files , reformat the drive (which would lock-out the bad areas of your drive so that they woudln't be written to), and reinstall everthing.
Another option is to try running another disk utility like Norton or TechTool. Disk Warrior is great, but is confined to only fixing directory issues, and not other problems which one of the other ones might.
good luck and let us know...