Wow, i bet that was not easy. I use Smart Defrag with excellent results >> click here
How to get back what you have lost tho must have been tricky. You could try a repair or do an sfc /scannow.
Put windows cd into the cd rom, close down any window that might pop up. Go to the run command box, if vista then type it into the search, then type this into the box >> sfc /scannow ,,, please note that there is a space after the sfc..