But physic yet could never reach The maladies thou me dost teach; (31-32)
The body makes no bones (get it?) about this emotional knowledge: it's bad and painful. By comparing it to diseases—and incurable ones at that—the body pathologizes emotions. In other words, it defines feeling as not normal and never good.
Whom first the cramp of hope does tear, And then the palsy shakes of fear; (33-34)
This is the body's first pairing of good emotion and bad emotion. But notice that there's no difference in opinion. The body feels exactly the same about hope as it does about fear: they both feel bad. What's up with that? Can the body really not tell the difference? Or do all emotions end up feeling the same way?
The pestilence of love does heat, Or hatred's hidden ulcer eat; (35-36)
The body's obviously put some time into thinking up appropriate metaphors that really capture the qualities of these emotions. It compares love to a "pestilence," which means some super-aggressive contagious disease (see: plague). And when you're in love, it sometimes does feel as if passionate crush-obsession is taking over your mind like some kind of monster rash. Hatred, on the other hand, eats away at you secretly, like a stomach ulcer, amirite?
Joy's cheerful madness does perplex, Or sorrow's other madness vex; (37-38)
Joy and sorrow are described as twin crazies, one making us so happy it's kinda weird and the other making us so sad it's really annoying.
Which knowledge forces me to know, And memory will not forego (39-40)
The "which" here is a relative pronoun or stand-in for all the complaints the body's just listed: the madness, the ulcers, the love-pestilence, the cramps, and the shaking. The emotional knowledge provided by the soul forces the body to experience all this stuff, while the memory (also operated by the soul) makes sure the body can't forget it.
What but a soul could have the wit To build me up for sin so fit? (41-42)
Soul, you better hide yourself. The body's been pretty peeved throughout this stanza, but in the final four lines, the tone becomes quietly devastating, full of these scary accusations. "Who but a soul" heaps contempt on that spiritual powerhouse, implying that only something as tyrannical and malicious as a soul could come up with anything this mean. By teaching the body about emotion and feeling, the soul opened it up to the possibility of sin. And that's a serious bummer.
So architects do square and hew Green trees that in the forest grew (43-44)
Here the body compares itself to a young tree that would have grown peacefully in the forest, producing acorns, providing a home for squirrels, living the forest life. Add a soul to this innocent story, however, and the future takes a sorry turn. Instead of flourishing naturally, the tree is shaped and trimmed into a box or a gazebo, forced into being something it doesn't want to be. The underlying point here is that without a soul a body would be more natural, like an animal, free of civilization and all its evils.