I feel like a broken record reiterating how good these episodes are, and how much insight you are both bringing to a (frankly) third-rate novel I'd have long since put down. But perhaps for praise, as for libel, the truth may serve as a defense. At least I hope so.
A couple of quick thoughts:
• I forget in which episode, but you already raised the possible parallel between the structure of Operation ARES and Book of the New Sun: you were too modest to note it, but that was followed through here as JC becomes the leader of Ares, as suddenly & unexpectedly as Severian becomes Autarch — also also, I think, far less convincingly in several different ways. But the plot is clearly in Wolfe's head: he just got better at it.
• Another BotNS parallel: you mentioned the various ways in which people give up their humanity, become partly human, more primitive, etc: this is more fully developed in the zoanthrops (the people who return to beast-like status) in Sword of the Lictor.
• Another possible interpretation of the Russian brainwashing is as a crude metaphor for communism: SF works at the time often paralleled communism using fantastical means of total control (Heinlein's Puppet Masters, Invasion of the Body Snatchers): given that they're literally Russians, it's hard not to see that as one element of what's going on here.
• I thought a couple of theology-savy people like you might have something to say about "power dwells in the heart"; it certainly struck me. But I have no insights into it.
• I thought it was worth mentioning the moment of fairly stark racism (of the "yellow peril" variety on p. 131:
…"I could have a hundred divisions of semi-illiterate Orientals armed with burp guns and hand grenades if I wanted them and could find some way to get them here. You are no Earthman, and you're from this part of the country. Would you like to see a force like that turned loose here?"
John shook his head. "I'd almost rather go over to Fitzpatric Boyle."
"So would I...."
Maybe I'm over reading. But I thought the "rather go over" remark, especially since both of them made it, given their various political commitments, rather striking. Not to mention the whole "semi-illiterate Orientals" phrase (granted that at the time, it was less true that "Orientals" was not the preferred nomenclature (Asian-American, please)). But I found it jarring.
Finally, although you mentioned it, I believe, for the first time since your opening episode on the book in this episode, it still struck me that you might make more of the fact that Wolfe's original novel was cut by 40%. (Has anyone ever tried to get him to publish, or at least release online, the uncut version? Does it still exist? I understand that GW has disowned the published version, but presumably he'd at least think the uncut version was better, even if still bad.) Several moments in these chapters felt, to me, like scenes were cut: the transition of John talking to Lothrop to trying to make mental contact with Anna was jarring — there didn't seem to be even a line break (although it was on a new page, so maybe it was just a formatting issue). But I wondered if pages might not have been cut there.
But it then occurred to me: one of the difficulties with this novel is that many of Wolfe's signature techniques are doing things that might otherwise look like bad craft deliberately. Not knowing Wolfe, simply omitting a major scene from a novel (the crisis at the gate in BotNS, say) might be thought to be bad craft: knowing Wolfe, it's a subtle style of storytelling. In other Wolfe texts, apparent contradictions are signs that we're missing something. And so forth. One needs to really trust the author to understand that these are deliberate, and not simple sloppiness.
But how, then, are we to read here? After all, here — in his disowned apprentice novel, which additionally was drastically cut by an editor — an omission could be craft, could be sloppiness, or could be bad editing. It makes it very hard to read Wolfe in particular knowing that the sort of clues one looks for here have such obvious other alternatives. Not to say that Wolfe is infallible: Even Homer Nods and all that (remind me to tell you about the actual mistake, and not clue, in Lolita sometime); indeed, one of the reasons that I (for all I, obviously, love it) and still skeptical about what I'll call the Wolfe/Nabokov mode of writing is that people are fallible, and that it sort of assumes a level of control that is, in practice, not attainable. Nevertheless, Wolfe usually can be trusted, at least as a first, second and third hypothesis; the possibility of simple sloppiness comes up only after one has sincerely made a lot of attempts to find intentional meaning, and even then is always provisional. Here, it's hard not to make it the first thought. It makes reading the book hard, at least for me.
Hence my all the greater admiration at how well you two have done with it. On to 9 & 10!