In Gods Go Begging, how do war and prison impact the characters and affect their ability to experience their lives? Use quotes from the text to analyze the metaphors and symbols, the tone and/or feeling of each scene, demonstrating its connection to your claims and arguments.

In the novel, the devastating effects of war and prison negatively impact the main characters. In my answer, I will discuss two characters from the novel: Jesse Pasadoble and Anvil Harp.
Jesse Pasadoble is a San Francisco public defense attorney who has to wrestle with some personal demons. As a Vietnam Vet, he consistently experiences the symptoms of PTSD (post traumatic stress disorder), which means that he struggles with disturbing flashbacks and frightening dreams on a frequent basis. Jesse also has difficulty connecting emotionally with his long-suffering girlfriend, Carolina. It is obvious that memories from a decades-old war still haunt Jesse, and are impacting his ability to forge deep connections with others.
For example, Jesse thinks that Carolina is beautiful but "excessively demanding." Carolina "wants a normal, healthy, loving relationship" with Jesse, but he is uncomfortable with a relationship on that basis. Jesse had always left previous girlfriends when "sexual demands gave way to emotional demands." Here's a quote that perfectly explains Jesse's struggle:

How could he ever explain this to Carolina...to anyone? The painful memories had evolved into a cold, quizzical passacaglia, eternal notes in basso profundo and in unbreakable code. Someday he would solve the riddle of it. Someday, he would live one sweet, mortal moment without the constant accompaniment of percussive anger and a grinding bass line of grief.

The tone of the above passage is somber and melancholy in nature. Jesse uses musical metaphors to characterize the pervasive consistency of his tormenting symptoms: "The painful memories had evolved into a cold, quizzical passacaglia, eternal notes in basso profundo and in unbreakable code." In music, a passacaglia is a solemn dance that originated from Spain in the 17th century. What's unique about a passacaglia is that it often contains what is called an ostinato, which is a musical motif that repeats itself throughout the passacaglia. The ostinato is usually performed in bass. From the passage, basso profundo is the lowest range sub-type of the bass voice; the basso profundo is strong, bold, and powerful in nature.
The passage above effectively uses auditory imagery to describe Jesse's torment; his terrifying dreams and flashbacks are continual, pervasive, and entrenched. Note the bold and heavy descriptors: "basso profundo," "passacaglia," "grinding bass line of grief," and "percussive anger." 
Now, we discuss the negative impact of prison in the novel. In the story, Anvil Harp is in prison for the murder of Princess Sabine's purported husband. Anvil admits to Jesse that he had always adored Princess Sabine, but he was unlucky in love. Sabine had turned down every single one of his marriage proposals. Later, the wrenching discovery that Sabine had bedded his twelve-year-old brother sent Anvil into a depression. Although he never held Sabine's unnatural desires against her, Anvil had been devastated by the knowledge that Sabine enjoyed preying on pre-adolescent boys. 
Anvil knows that he must resign himself to serving out the rest of his sentence, and he is philosophical about it. In fact, he doesn't regret killing Princess Sabine's husband. Like others who have been incarcerated, Anvil knows that he cannot erase the past; it will continue to haunt him for as long as he lives. Here is how Jesse describes men in prison:

Jesse Pasadoble knew that those men lying down up there were all stuck on cruise control, going from place to place without any discernible motion. They moved from county jail to state prison to federal prison and even to death row in the same insensible condition: half-alive and half-asleep, moving only in the fourth dimension.

In the passage above, the tone is one of despondency. The prisoners languish in prison; they are "stuck on cruise control" and have ceased to approach life with any vestige of hope. They are neither dead nor alive, operating only in the "fourth dimension." Here, the author uses the "fourth dimension" as a metaphor to characterize the hopeless condition of the prisoners. The experience of being incarcerated is devastating to the men and far removed from the scope of any normal human experience.