Well, keep in mind that Jacob is the narrator of this novel who is entranced by his grandfather's outlandish past.  With this in mind, there is no doubt that there are many quotes that "show a struggle" as you ask in your question.  What follows are just a few.

First, we have Jacob's struggle with the unknown.  Take a look at this quote:

There was romance in the unknown, but once a place had been discovered and cataloged and mapped, it was diminished, just another dusty fact in a book, sapped of mystery. So maybe it was better to leave a few spots on the map blank. To let the world keep a little of its magic, rather than forcing it to divulge every last secret. Maybe it was better, now and then, to wonder.

In short, Jacob Portman spends the entire book trying to figure things out and get them straight in his mind; however, he constantly fights with himself about the possibility of not knowing, or not being able to know, something.  Jacob can never truly understand the peculiar children, even when he finds that he is one of them, himself.  Here Jacob admits that there is a certain alluring quality in the unknown things of life.  Sapping the unknown of its mystery somehow takes away its beauty.  Jacob determines, then, that it is better simply "to wonder" about things sometimes.  This quotation absolutely, and poignantly, pinpoints Jacob's struggle with this unknown mystery.

Next, comes Jacob's struggle with "monsters," not the monsters of make-believe, but the monsters of real life.

But these weren't the kind of monsters that had tentacles and rotting skin, the kind a seven-year-old might be able to wrap his mind around--they were monsters with human faces, in crisp uniforms, marching in lockstep, so banal you don't recognize them for what they are until it's too late.

These are the true monsters of the world, humans that are much more than "peculiar," ones that have an evil purpose of death and destruction and desolation.  Here Jacob (although he doesn't say so) vividly describes the army of any dictator:  Hitler, Stalin, Mao, etc.  Blind followers, blind and human followers, who kill without thinking.

Also in regards to his grandfather, Jacob contemplates the struggle of good vs. evil.

To have endured all the horrors he did, to have seen the worst of humanity and have your life made unrecognizable by it, to come out of all that the honorable and brave and good person I knew him to be— *that* was magical

Here is Jacob speaking plainly about his grandfather.  Now Jacob knows how much his grandfather has seen and the true "monsters" that his grandfather has come to face.  Through all of this, Jacob is amazed that seeing all of these horrors could result in such a "good" and a "brave" person as his grandfather was.  Of course, Jacob thinks of this as the one truly "magical" thing he has witnessed.  How do we know it was true struggle by Jacob?  Because he says he has vivid nightmares where he wakes up "crying hot stupid tears" about it and specifically about "wasted bodies being fed to incinerators."  One can think of no worse nightmare.

Finally, one of the most ethereal of the struggles of the book has to do with Jacob's struggle with appearance vs. reality (one of the prominent themes). I will leave you with a quotation that speaks for itself and, further, screams of this theme:

We cling to our fairy tales until the price for believing in them becomes too high.