Stanza 3 Summary

Get out the microscope, because we’re going through this poem line-by-line.

SOUL
What magic could me thus confine
Within another's grief to pine?

The soul's got the mic back now, and its mood is 100 percent unimproved. Still addressing some unknown other, it wonders what kind of supernatural force has the power to keep it inside this body, feeling all its pains.
Notice that the soul says "magic" and not something more expected, like "God" or "heavenly decree." Souls pal around with God, right? And hasn't the soul been hinting all along at getting back to heaven?
"Magic" is a pejorative (negative) word here, a deliberately rude way of referring to the soul's relationship with the body. This soul may hang with the celestial harps, but it's sure as heck not going to dignify the body with any of that religion. That would mean everything was on purpose!
Plus, this may be a subtle verbal payback for line 20, where the body called the soul an "ill spirit." If the body thinks this is all a terrible spook-show, then the soul's going to play along.

Where whatsoever it complain,
I feel, that cannot feel, the pain;

In the first stanza, the soul was all upset about the actual fact of being inside a body, tangled up in anatomical structures. Here it's zeroing in on some genuinely unpleasant stuff: it has to feel the body's physical pain, no matter when or where.
What really cheeses this soul off is the fact that by itself it can't feel anything. That's right: no aches, no cramps, no middle-of-the-game pulled muscles. It's only when it's trapped inside the body that the soul's forced to become conscious of these pains.
That's what makes the paradox of line 24: the soul can't feel (on its own), but in the body it can feel.

And all my care itself employs;
That to preserve which me destroys;

Get a load of this body's wiliness: the body mooches off the soul—its consciousness, its judgment, etc.—to keep itself healthy.
It's kind of like the placebo effect. As long as you think this pill (that is actually a Jolly Rancher) is genuine medicine, you can actually get better. To the soul, that's just plain unfair.
And as you might expect, the soul spits out a bitter paradox about this, noting that the body preserves itself by destroying the soul. How's that? Remember, this soul-dude wants out—once the body dies, it's gonna peace out. The longer the body draws upon the soul's consciousness to stay in good shape, the longer the poor soul has to put up with being trapped down on Earth.
To put in another way: good health = unhappy soul.

Constrain'd not only to endure
Diseases, but, what's worse, the cure;
And ready oft the port to gain,
Am shipwreck'd into health again.

Like a stuck record, the soul stays on this theme for the next few lines, spreading the paradox and metaphor on like garlic paste on bread. Only garlic bread makes people happy and the soul, as per usual, is anything but.
Not only does it suffer through diseases; it also has to endure the cures. In other words, it experiences all the discomfort of a fever and then the disappointment of feeling Tylenol PM narrow its chances of death-escape back down to zero. Buh-mmer.
Did you pick up on that nice W alliteration in "what's worse"? Yeah, well the soul wanted you to—anything to get your attention, and your sympathy.
To drive home the point, the soul hits us with a neat little paradoxical metaphor: the soul is a ship that's been sailing the deep blue for several years, buffeted by titanic waves, trudging through windless sea-deserts. (Think Holland America on steroids.)
But here's the bad part. Whenever a port is in sight, a sudden storm sweeps the ship back into the sea.
With its metaphor-clothes off, the sentence looks like this: whenever the body is teetering on the edge of death and the soul's poised to fly away, the healing process kicks in, the body gets well, and the soul is forced back into its life of captivity and pain.