After you've recorded the album side, save it to disk in the program's native format (e.g., wav or aiff). My files run about 270mb or so per side.

Finding the song breaks is easy, look for the drops in the histograms. Cut and paste each song into a new file, where you'll clean up the individual song.

There's a lot of programs that remove pops and scratches on the market. Unless you're willing to pay $1200 or so, don't bother. The cheaper software squelches highs, adds weird artifacts and distorts the overall feel. In many cases, you can hear the classic 'pumping' of bad compression settings.

I edit by hand, and truth is, I leave all but the most aggressive pops in. When the band is loud, the scratch is barely noticeable. Quiet sections are a pain. If you've cleaned your record well, the sound quality will be decent. The Harry Marchard album, for example, the disk was covered with green mildew.

To remove a scratch or pop, locate it on the song. Listen to it, is it worth removing? If so, zoom in close enough to select the tightest area of the wave. With SoundStudio, I have an 'interpolate' command that averages the two selection points together. In other programs, I grab the pencil tool and draw the wave myself. That's it! Done.