The sound editing apps available now are superb - I use Sound Forge4 which is not the latest but has more whistles and bells than I can use. What I found useful was to be able to mask or filter-out the hf on the inbreath of my own songs, though I have found it is advisable to leave enough in otherwise the listener feels there is something missing.
The CDex ripper does the job as good as any. With your 40 Gig HD there should be no problem with space so save key versions of the WAV's & don't throw away the interim files until you are totally satisfied .