I have a sin of fear, that when I have spun My last thread, I shall perish on the shore;
Now we're talking about a very specific sin, unlike the general sins of the stanza before. This sin is the sin of fear.
So, what's our speaker afraid of? It looks like it's dying, a.k.a. spinning his "last thread." He's using a metaphor to compare running out of life to running out of thread while spinning yarn (both are major bummers). When it's gone, it's gone.
He's not just afraid of death, either; he's just afraid he'll die "on the shore" between heaven and hell.
Yep, that's another metaphor. This time, the area between land and water is a metaphor for Limbo, the place some religious traditions believe exists for people not ready for heaven but not quite fit for hell, either.
Donne's speaker wants to get to heaven, that's for sure. And in order to get there, he needs forgiveness. That's why he keeps asking for it.
Notice that we've abandoned the "Wilt thou" that began the 1st and 3rd lines of the previous stanzas. This stanza is meant to read as a departure from those requests; something different is going on here.
But swear by thyself, that at my death thy Son Shall shine as he shines now, and heretofore;
Ah yes, the speaker's finally got a new request for God: he wants Him to swear (by Himself, no less) that Jesus will continue to "shine" on his life, the way he has "heretofore" (before now).
Er, so what's that all about? In Christian tradition, Jesus's death on the cross represents ultimate forgiveness for those who accept Him. Jesus is kind of like an intermediary between God and man.
If Jesus stays in his life, then, the speaker won't wind up in Limbo. He believes he'll be forgiven of his sins and thus let into Heaven.
Notice the wordplay going on here. By having the "Son" shine, he's connecting God's "Son" to the actual sun with a pun. Tricky guy.
What's not tricky, though, is the rhyme scheme in this stanza, which seems to be keeping in line with the pattern of the previous two stanzas. Check out "Form and Meter" for more.
And, having done that, thou hast done; I fear no more.
The poem began with the speaker questioning God and worrying about sinning. Now, in the final line of the poem, the speaker says he "fear[s] no more." So what caused this change?
The short answer is God's forgiveness, via Jesus. The speaker believes that this Jesus is his only chance to get off the "shore" and into heaven.
Notice that everything is in God's hands; the speaker seems helpless to save himself from Limbo. He calls out to God to have His son save him. Does the speaker have no power in the situation? Is he saying that humans have no power over their own fate?