Are they created from scratch, or do they use some parts of the original music?Well I certainly cant speak for everyone that creates them, but all mine use audio files directly from the games such as a rip (and in general most custom soundtracks do.) To answer you question, yes, the music comes from the game itself.
How much (how many songs) of the original music do custom soundtracks cover?Well even some of the best original soundtracks that are released commercially don't contain all the music within the game, so this is a misleading question. But generally your looking at anywhere from 14-25 tracks for custom soundtracks. At least thats how much mine average. Could be more could be less, and most of the music covers the majority of the game.
How faithful are the custom soundtracks to their respective games' music?I would say they are very faithful, however, this all depends on what type of music is within the rip. Sometimes as many know, rips can be very repetitive, often containing the same tracks two or three times. Now you can make a decent soundtrack out of that with the proper mixing, but again, it all depends on the rip.
Also I should note CrazyFox that most custom soundtracks are made because of the fact that the respective game has gotten no official release. Me personally I would much rather listen to a "custom" soundtrack, or something that resembles and official release then listen to 150 tracks. Custom soundtracks are meant to take rips to games and create a more enjoyable listening experience. Hope this answers your queries.