"Among all jewels judges wise
would count her best an hundredfold"
Here, the father is speaking about his child. He calls his child a "pearl," representing how valuable and precious they were to him. In this passage, the father tells us that among all the jewels in the world, his child was the most valuable of all.
"Alas! I lost my pearl of old!
I pine with heart-pain unforgot"
In this passage, the father tells us about the loss of his child, calling them a "pearl." He tells us that he "pines" for this loss, with a "heart-pain" that is "unforgot." By this, we understand that the father's grief is persistent, all-consuming, and seemingly has no end.
"O Earth! a brave gem thou dost stain,
My own pearl, precious, without spot!"
At the end of the second stanza, the father exclaims "O Earth!," expressing his devastation about the loss of his child. He tells us that his pearl is "precious, without spot," alluding to the innocence of the child, and the fact it is unfair that an innocent person has been seemingly punished with an early death.