Decaying more and more, Till he became Most poor: (3-5)
Life outside of Eden is just one bad thing after another. The accumulated badness transforms Adam from a just-created dude with everything to a poor and miserable man. "Decaying" sounds more like corpses on Halloween than hoppy bunnies on Easter, driving home the negative transformation that Adam is undergoing.
With thee O let me rise (6-7)
The speaker begs God to let him rise out of Adam's sin and transform himself from a miserable sinner into an adoring Christian. And hold on to your iambs, we've got a parallel transformation in line length. Notice how the shape of the poem mirrors the changing content. When Adam and the speaker become thin, poor, and despairing, the stanza also contracts, from 10-syllable to 2-syllable lines. And when the speaker's on the upswing, feeling great and soaring high, the lines get correspondingly bigger, from 2 back up to 10 syllables.
Thou didst so punish sin, That I became Most thin (13-15)
Borrowing "became" from line 4 in the first stanza, Herbert reemphasizes his bad-to-worse transformation. Being born with Adam's inherited sin is bad enough, but once God gets in on the game, punishing him with "sicknesses and shame" (12), Herbert wastes away. Line 15 marks the low point, in both Herbert's life and line length: Herbert is "most thin" and things aren't looking good.
With thee Let me combine (16-17)
But just as in the first stanza, the transformation is reversed. Herbert asks to "combine" with God, acknowledging that by himself he's too weak and damaged to turn his life around. At first "combine" seems like a general verb, but it gets a more specific meaning in the last two lines. It's clear that Herbert can't go it alone. He needs to join with God in order to transform himself into something new.
For, if I imp my wing on thine, Affliction shall advance the flight in me (19-20)
Let's get down in the feathers, folks. Here Herbert gets all nitty-gritty with his bird metaphor, and "imp" gives some precision to the idea of combining with God. Not only does the speaker want healing ("to imp" means to repair); he also wants transformation. He wants to incorporate some of God into himself, to borrow some of God's holy substance (or, in the metaphor, his feathers) to bulk up his soul.