Hello.
I love the sense of yearning in this song – it's embedded deep. I do hope you're feeling better now!
Your melody operates so that the first two lines of a verse are the call and the last two the response. This means it works when you have one idea for each half, or one idea developed through all four lines. But I'm not sure it works when you have one idea for the first three and another for the fourth, as in:
I feel like a faded flag
In a cold, cold wind
Blowing on a silent sea
I need a new friend
The melody makes me connect the last two lines as one idea, which of course doesn't make sense. This may be fixable just with phrasing, though...
I don’t think the "skin / in" rhyme works. Partly because the word white is pretty much redundant, so its inclusion almost makes it sound like you're bragging about being white! And also because you're reversing the natural stress of "white skin" to match that of "dreams in", which is slightly awkward.
I love the chorus, and the subtle way you progress from alliteration to half-rhyme, to merely second-syllable feminine rhyme supported by rhythm. The melody and lyrics work beautifully here. And I love how the guitar drops out before "safe harbour".
But what I'm not mad about is the immediate repetition of the chorus – even though it's a nice melody, it feels like a finished melody, with no need to repeat it. Maybe you could try putting the "wondering / thundering" couplet between the two halves. I know you've used it to introduce the chorus, but I think the chorus is strong enough to be self-introducing; it only needs some help the second time. (Having said this, the issue went away for me after the third listen.)
By the way, I love the internal rhyme on that "wondering" couplet.
In the Maine verse, it’s not immediately clear that the pines are speaking directly, so when the word "you" arrives, I was momentarily taken out of the song. I think it might be clearer if you use reported speech:
On the shores of Maine
The pines still whisper
That she returned again
And I just missed her
Regarding instrumentation, I wouldn't mind some accordion in there for a sea-shanty sound... (This may be an insane suggestion.)
I think my favourite part is the way you build so powerfully into "I need safe harbour" using only two lines. That's strong writing.
Matt