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.

In Gods Go Begging, how is time altered or diminished during war and in prison?

When Jesse visits the prison, he goes to the ward in which the prisoners have to remain recumbent. In this strange environment, it's almost as if time is slowed down. Véa writes that the prisoners "clung to their thin bedding and small cots in the same dull way that stunted, unmetamorphosed caterpillars might cling to their ill-woven cocoons" (53). In this sentence, the prisoners are compared, using metaphor, to caterpillars who remain in their cocoons and never burst out of them. Instead, they remain inert in their beds, and the prisoners' beds become "finely tuned machines capable of travel through time and space" (53). The author compares the prisoners' beds to space ships, implying the eerie mood of the ward in which the life-giving or energy-giving potential of time is removed, leaving only a kind of void.

The author also implies that the death caused by war and violence makes time slow down and sucks it of its energy-giving potential. The two victims of violence who lie on the street in the first page of the book are compared, in a simile, to soldiers. The author writes, "Then, like warriors abandoned on a field, they lay in unearthly calm as the things of life deserted them" (1). When they die, time is suspended for them. They are able to calmly watch as they are transported to the medical examiner's office, as time no longer has any urgency or meaning to them. Instead, the death caused by war and violence slows down time.

In Gods Go Begging, how does time change in war and prison?

Time slows down in the prison scenes of the novel, and while the body is inert, the mind travels. Véa writes of men in prison:

Their beds were geared for long distances, for trips to Alpha Centauri and the Sombrero Galaxy. Everyone doing time knew you had to sleep away the years in a state of suspended animation in order to reach your destination alive. (53)

Véa uses a metaphor comparing time in prison to time spent suspended in the darkness of space. The prisoners' beds are compared to space ships, and prisoners who hope to get out of jail spend their time in a state of inert waiting for their dark journey to end. While they are in jail, they spend time dreaming and sleeping. Véa writes:

For most prisoners, the bed, powered by a decent pillow, would merely calculate your good time credits automatically and wake you up when your time in the stir was done. (53)

This passage also uses a metaphor in which the bed is compared to an alarm clock that will wake up the men after they have spent their prison time dreaming. The mood of these passages is one of dread and waiting. 

In war, however, time speeds up so that all of life can be compressed into one second. The protagonist, Jesse Pasadoble, fought in Vietnam. He recalls how fear can make one moment seem like an eternity. Véa writes:

A year and a half of incredible fear in the highlands of Vietnam had been transformed into an almost anguished love of the living, intact moment, the moment that can never be possessed. (45)

In other words, from living with constant fear while fighting in Vietnam, Jesse comes to regard each moment of life as a precious eternity. Véa implies that fear makes Jesse treasure each moment as if it held all the mystery and majesty of life. In war, time is sped up so that the soldier tries to experience all of life in one moment.