As with almost every song on Out of the Cradle (by the way, love the Walt Whitman reference there!), I believe Lindsey is talking about leaving FM. Time is passing, "the ticking of the tock," and he hasn't gone yet - "things left undone." But he will soon - he's got to get away from the "darkness" of FM and "fly into the sun." This theme is expressed very similiarly in Don't Look Down, and it pervades the album. Oddly enough, Stevie uses the same wording in Straight Back years before on Mirage, but she's urging Lindsey to return there! Was this intentional irony on Lindsey's part? Probably not, but you never know. In this song, he doesn't know why he's waiting; he knows he has to do "what [he] can" to keep himself sane and to him, that means leaving FM.
I think this song may be about trying to deal with feelings of insecurity, fear, depression - all summed up as "darkness." Judging from his whole body of work, these are feelings he's dealt with most of his life and they're weighty feelings that can sometimes get on top of him, especially as he tends to keep them inside where they build up. I dont really see this relating to his leaving FM as much as just being about life in general. I think he's trying, through the use of vivid and disjointed images, to paint a picture of what it feels like (the ill ease, the paralysis, the claustrophobia of such feelings) and explain that he's doing the best he can to get out from under ("when the darkness comes you've got to fly into the light").
In an extended view of this theme, I look at this song as an older, wiser man coping with and trying to find avenues out of the "darkness" he first wrote about in "I'm So Afraid." He's not sure how things will get better (as the "what will be will be" leaves the future somewhat ambiguous), but he still sees that as the better alternative to staying in the, by now, way too familiar darkness.
An underlying theme here seems to be about being allowed to deal with these things in his own way.
When the darkness comes
You've got to do with what you've got
I'm doing what I can
The process may not be tidy and sweet, but he's doing the best he can under the circumstances and that's how it must be. Nobody can solve these problems for him and I don't really think he wants them to. He doesnt need advice or scolding, he just needs some understanding that he must deal with this on his own terms.
This is a pretty good song...but I'm surprised that nobody mentioned how similar-sounding it is to "Big Love".Though I doubt there is a parallel in lyrics between the two songs...maybe this is a context clue? A little hint of Fleetwood Mac? This is partly why I agree that this song is about Lindsey leaving FM. Lindsey is saying that FM was great for a while but then "darkness comes". So he has to "fly into the sun" to escape the darkness (because "the sun is bright") and he has to "do with what [he's] got" to cope and remain sucessful.