msconfig re: reconfiguring boot.ini

I had serious virus issues partition(1) would boot and then immediately shut down. I found a resolve in a forum here and was able change the boot.ini to partition(2).

I obviously only had half of the steps.

I lost all my ms office software and when I reinstalled them they are now unregistered. I lost all my games, I did not loose my downloaded music however, most of them will not play because of a copyright error.

Is there steps to correct this?