Do you have a ComboFix log?
I'm glad that you are so certain that ComboFix is at the root of your problems...I'm not
. Faulty sectors on a hard drive don't necessarily mean the kiss of death...but it's certainly indicative of something which may be unrelated to ComboFix or malware.
If it were my system...I would run the appropriate hard drive manufacturer's diagnostic, before I expended any energy on anything else.
But since it's your system and you seem convinced that all is due to malware and running ComboFix...I suggest that post your CF log (if you have one) at BC Malware Removal Logs Forum, after reading the following
: ComboFix usage, Questions, Help - Look here - http://www.bleepingcomputer.com/forums/topic273628.html
If you don't have a CF log that you can submit, then I suggest that you follow the suggestions at Preparation Guide, Before Using Malware Removal Tools and Requesting Help - http://www.bleepingcomputer.com/forums/topic34773.html
, taking care to note the correct forum for posting the requested logs.
FWIW, current backlog for malware log topics approximates 7 days. If you are seeking a quick solution/resolution...then you may want to run the hard drive diagnostic before making your decision as to what your next step should be. There is little point in attempting to reinstall Windows, IMO, on a hard drive which may have problems.
Note: A repair install effort...is never guaranteed to resolve system problems...it is merely an effort. It cannot overcome malware or hardware issues and is not guaranteed to overcome every system issue (e.g., partition issues). It is not equivalent to a format/clean install which wipes the board clean and makes it easier to try to pinpoint any issues which subsequently arise/appear.