I recently aquired a computer that needed a little cleaning. To free up some
of the memory I ran the disk clean up tool...then I deleted some unwanted
programs...then I ran the defrag tool and up to that point everything seemed
to be working "Okay." When I ran the error-check tool it found some errors.
After running it again and asking it to fix the errors it deleted something
like four indexes (not sure of numbers at the moment, will need to look at
log if necessary). Anyway, System will not start up normally anymore, I get
an unexpected shut down and it takes me the prompt to start in Safe Mode etc.
It will only start in Safe Mode and System Restore has no effect?

What have I done and how do I recover from this mistake?