Many people (including myself) had issues with the Custom 3 fit, as well as the cable. These combined were a deal breaker for me. Later on, I ended up getting the S4 and preferred them to the Custom 3, largely due to the fit. The build quality is very similar and both IEM's use the same strain reliefs.
In terms of their sound, the Custom 3 is much more detailed and crispy sounding, with enough low end to satisfy all but those who are bass heads. The S4 has the punch and slam which the Custom 3 lacked due to its being a dual BA. However, just because the S4 has much more bass, doesn't mean it doesn't have the Klipsch highs, it is a very bright IEM. The highs are just not quite as resolved as the Custom 3, sounded slightly more colored and sparkly to me. The mids of the S4 are not as detailed as the Custom 3, and may be slightly more recessed.
Also, keep in mind that the Custom 3 was not designed for the same consumer market as the S4 was. The S4 was compressed audio files in mind, being listened to by the average consumer, and will sound more forgiving and less analytical sounding. The Custom 3 was designed for musicians.