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 "Presbyterian."

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Shrug emoji. All Christian denominations are the same thing to me! This probably indicates something to somebody who grew up in the Midwest or the South. But I grew up in the San Francisco Bay Area in California. I'm a fucking heathen. Nobody ever taught me what all the differences to all the denominations were!
    The extent of my "religion" was being baptized when I was born (my mother is, technically, Catholic. My father is one of those other ones) and being forced to go to one Sunday School class when I was about six during a trip to visit my uncle's wife's family in Salina, Kansas.

So I did the most minimal research possible on Presbyterianism (which means I read the Wikipedia article until I found something that ties it in to Pynchon's themes across various novels). I learned Presbyterianism was greatly influenced by John Calvin who believed in predestination. He said, "All are not created on equal terms, but some are preordained to eternal life, others to eternal damnation; and, accordingly, as each has been created for one or other of these ends, we say that he has been predestinated to life or to death." Pynchon seems fascinated with the idea of predestination, mostly in the idea that if one believes in it, one must hold in their hearts the belief that most people, including themselves, can do nothing to attain God's grace. They are damned at birth. The only hope is that they aren't damned at birth (which seems like a pretty major narcissistic hope). In Gravity's Rainbow, he uses the term "Preterite" to describe those destined for death. Here, he brings it up with one mere word. In Mason & Dixon, he brings it up in line 38, page 9, when he invokes the names of Wesley and Whitefield, the founders of the Methodists who had a falling out between them regarding predestination. I can't speak for his other books having either not read them or read them over twenty years ago (The Crying of Lot 49).

That's probably more than enough to write on one word.

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 "Penance? You'll do that anyway. You're not Catholic, Mr. Basnight?"

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Sometimes making oneself a better person is too hard. It's easier to just take a dozen lashes with a whip and be done with the guilt of your sin. But as Drave correctly points out, atonement and penance are not two variables in different equations; they're values on the same side of an equation balancing out the other variable, guilt. Lew will rightly punish himself for having hurt his wife which will probably lessen the amount of time atonement will take. Without penance, atonement just takes the standard amount of time that needs to pass before grief isn't in control anymore. You really don't have to do any work; time will do it all for you!

"You're not Catholic"
I don't know enough about Catholicism or any other Christian denomination to understand why Drave brings this up. I think maybe it's because Catholics rely on penance to atone for their sins? Having to say a bunch of Hail Marys and rubbing rosaries and such? While protestants don't care about ritual penance so much as just repenting to Jesus? Seriously, this shit really is nuts to me, a person raised areligious who mostly learned about these things through television, Sunday Christian puppet television shows, and a few courses in college.

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 "What if I didn't care what it took to bring her back?"

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Here we go! "What if I can just skip all the hard work and sell you something extremely valuable instead? Like . . . oh, I don't know . . . you into souls, Drave?"

Also, this is probably why Troth doesn't want to come back, Lew. Because you believe she doesn't have a choice in the matter. She's gone. She isn't bound by whatever wild scheme you can come up with to drive her back in your arms. She has agency, you know!

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 The soles of Lew's feet began to ache, as if wanting to be taken all the way to the center of the Earth.

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This sentence is probably supposed to make you think of Lew going to Hell. It references Lew's "soul" with a homonym and the center of the Earth where Hell is figuratively located. It's also possible Drave's admittance that he "can't speak for God" was an indication that he's definitely the devil. So now I'm wavering back toward Lew being in The Twilight Zone over Lew having succumbed to the Scientologists.
    I suppose it can be both because art is hilariously subjective! Especially when the audience knows the author will never proclaim their intent! Good move, Pynchon!

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 "First of all," he advised, "I can't speak for God, but your wife is not going to forgive you. She's never coming back. If that's what you thought the payoff here was going to be, you need to re-evaluate."

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This line made me think of Memento. The main character in Memento is purportedly looking for revenge against the person who killed his wife. But, if the evidence we're given as viewers is to be believed, he killed his own wife, accidentally because she didn't believe his amnesia and risked her life testing him. So in actuality, the man should be looking for atonement. But if he believed that, what good is repeatedly making himself believe a different person has killed his wife just so he can hunt them down and kill that person? It's like the philosophical quandary about how much pleasure one gets from beating a horse that's already deceased. He explains that he has one spot on his body for his final tattoo, the one that declares he's done it when he gets revenge. But we see he's not getting revenge and when he kills, he simply sets up another jerk, and he's never getting the tattoo. The only time we see him with the "I've done it" tattoo is when he fantasizes about having his wife back. That's all he wants. And since that can't happen, he's lost himself in a revenge fantasy loop that keeps him feeling like he's moving forward and accomplishing something. But he's not moving forward; he's moving backwards. It's just that he can't move backwards quite far enough to bring her back.
    (Caveat: I've only seen Memento once, in the the theater when it came out, and I've never read any essays or reviews of it. So take my opinion with that grain of salt or whatnot.)
    Anyway, this line reminded me of that because Drave seems to sense that Lew doesn't give a shit about atonement. He's just looking to get Troth back.

"I can't speak for God"
If Lew's wife isn't going to forgive him then God had better or else why bother atoning at all? I suppose if we want to get all daytime talk show about it, Lew needs to forgive himself. But since he doesn't know what he did and seemingly is never going to, maybe he should just forget it altogether? Hmm, wasn't that Drave's suggestion in the first place? I suppose it was but the implication was that Lew can only move on with the help of Drave and his community.

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 Now and then, unannounced, Drave showed up to review Lew's progress.

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I'm not sure Drave's program designed to help with atonement is much of a concern to Pynchon because we haven't received any details about the steps Lew is taking towards atonement. It's probably because getting too specific would narrow the analogy. It's better to be vague so that the reader can choose what terrible and controlling self-help group or religious camp Lew has fallen in with.
    It's also possible Lew doesn't understand the program or has not been taught any of the steps. He's just out there doing chores for a bunch of strangers who occasionally give him a performance review or beat him with the remembrance stick.

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 Out the window in the distance, contradicting the prairie, a mirage of downtown Chicago ascended to a kind of lurid acropolis, its light as if from nightly immolation warped to the red end of the spectrum, smoldering as if always just about to explode into open flames.

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"contradicting the prairie"
So instead of horizontal and boring, Lew's view was vertical and exciting!

"a mirage of downtown Chicago ascended to a kind of lurid acropolis"
I guess his view is mostly of the light of Chicago, shining up above the city. So he's seeing not the city but "a mirage" of the city, kind of floating up as if some kind of fortress on a hilltop, lurid due to the display of lights. Possibly he's also seeing a "Fata Morgana" of the city.

"its light as if from nightly immolation warped to the red end of the spectrum"
Light shifts to the red end of the spectrum when moving away from the viewer. Does this mean Lew or Chicago is moving further from the other? Or is this just meant to say the light of Chicago, which is normally the regular old yellow color, seems redder as it escapes the city, making the city look less like a city and more like something burning?

"smoldering as if always just about to explode into open flames"
Okay, not burning, not yet! But smoldering! As if Chicago is a powder keg just about ready to kick off and show the world something spectacular.

Whatever this description ultimately means, it's definitely a reminder of the time the whole city burnt to the ground in 1871. I doubt Lew's recount of his life before coming to work with Nate Privett's detective agency takes place over twenty years prior but if so, Lew might be having a prophetic vision in this scene! Nah, Lew is definitely not in his forties when he winds up on the Inconvenience. He's referred to as a young man at the beginning of the section and in no way would even a man of Pynchon's age, nearly 70, when he wrote this think of a forty year old as a young man. No wait. A seventy year old would almost certainly call me a young man in public even though I'm nearly fifty. But I don't think a writer would describe a middle-aged character as young. That would simply be poor writing.

This description of Chicago, contradicting the prairie, is certainly one of potential energy, a vision of urban life and newfangled technology ready to propel us, through an explosive release of that potential, into the future.