I think what he means by "I'm literally dying without you here" is that "every second that goes by" is "one more second off his life" - in other words, every second he is one second closer to the death, which is inevitable, so he wants to spend as much time with the girl (I'm taking this song to be about a girl because G-d is everywhere, so the "miles and the hours" couldn't really separate anyone from Him) as he possibly can.
I think what he means by "I'm literally dying without you here" is that "every second that goes by" is "one more second off his life" - in other words, every second he is one second closer to the death, which is inevitable, so he wants to spend as much time with the girl (I'm taking this song to be about a girl because G-d is everywhere, so the "miles and the hours" couldn't really separate anyone from Him) as he possibly can.