I think the most obvious and straight-forward way of thinking of "not everything" is 314. But I agree with you, it is the general theme for S3. There are a lot of losses, but what is lost is not everything to the person.
Another example is Ben and his steroid use. He is feeling weak and down because his former partner died from AIDS, and turns to doping because he feels that he has lost everything, including hope. Michael shows Ben that he has not lost everything, especially hope.
I'm not sure I could define a particular character, or pair, who experiences "not everything" the most strongly, because they all experience it in different ways. That is one of the many reasons I love S3, because there are so many ups and downs. Also because the lows are so low that the highs are wonderfully high!