I’ve noticed a number of things about the Paul Rubin ciphertext, which are definitely beyond what the FBI’s cryptanalysts managed to find. Please feel free to advance these yet further!
The Paul Rubin Ciphertext
Here’s my transcription, as posted on the Cipher Foundation website, but with the individual lines numbered:
 digIs sawthn'g mathUlley-Dulles crancklavn' meteore iElli  zheaopfvamn greA'Lltenmn  kKiqtu albawmnabs dzhjellEiE matel ungdreabozvmie oie  sprekln meIktrene fodroscolmn oeir  *driEk Conant astereantol Iyvondiolon  desceth megleagna mAlzbourgnion grele  newtdo sfoatzdexklagh 2pont ¼ly asgestaltverbensdi  7469921  100.011x100.10x.10011.1.xx0.101.x.001011.101x1011.1001..10x1  01.001011x10.1x.11101.x1.001x1.001001  0.101.x.101110.x101.1101101.0101x1.1011  Want: datum Tywood Janossey Ketelle  R-QR6  aliacaui PER
The Last Two Words
It seems almost certain that “PER” stands for “Paul Emanuel Rubin”, which gives us a reasonable amount of confidence that this is a real ciphertext Rubin himself had made.
Rubin liked reading science fiction, and repeatedly claimed to be a member of a “Brooklyn Astrophysics Society”: however, despite asking a lot of people, the FBI were unable to turn up any reference to any such society – Rubin seems to have dreamed this up completely. So there is (I think) good reason to suspect that we might find obscure references to science fiction and/or imagined science embedded in this ciphertext.
And in fact this is exactly what we find on line . The word immediately before PER – “aliacaui” – comes from a 1950 novelette by Poul Anderson called “The Helping Hand“, that first appeared in Astounding Science Fiction:
Valka Vahino sat in his garden and let sunlight wash over his bare skin. It was not often, these days, that he got a chance to aliacaui… What was that old Terrestrial word? “Siesta”? But that was wrong. A resting Cundaloan didn’t sleep in the afternoon. He sat or lay outdoors, with the sun soaking into his bones or a warm rain like a benediction over him, and he let his thoughts run free. Solarians called that daydreaming, but it wasn’t, it was, well — they had no real word for it. Psychic recreation was a clumsy term, and the Solarians never understood.
In the story, “Aliacaui” is a central concept to the Cundaloans, one which the hard-working Solarians (machine-culture humans) find difficult to grasp:
“For instance, just this matter of the siesta. Right now, all through this time zone on the planet, hardly a wheel is turning, hardly a machine is tended, hardly a man is at his work. They’re all lying in the sun making poems or humming songs or just drowsing. There’s a whole civilization to be built, Vahino! There are plantations, mines, factories, cities abuilding — you just can’t do it on a four-hour working day.”
So this is the single word from the Science Fiction universe that Paul Rubin valued so much that he used it as a farewell in his note: “Aliacaui”, meaning lying around “making poems or humming songs or just drowsing”. Really, you couldn’t make it up.
The Codebook Indices
I’d also immediately point out that lines - almost certainly each use a different codebook entry, and that the seven codebook indices for them are on line  – 7469921. It seems likely (though not yet proven) that these are the indices in the order the lines appear.
Furthermore, lines - each almost certainly use a different codebook entry, and that the four codebook indices for these are on line  – R-QR6.
Hence, the three “binary”-like lines would seem to be codebook entries “R-QR”, while all the other lines’ codebook indices are digits: 7469921 and 6. I pointed this out to Craig Bauer before his book came out, but it was (alas) too late to update his Paul Rubin chapter.
Still, knowing this should help us avoid many pointless cryptanalytical tests: for example, there would seem to be no point in carrying out any test that combines a binary-like line with a text-like line, because they would seem to be using completely different types of codebook.
The Three Binary-Like Lines
If the 0s and 1s in these lines are binary, I noticed something a little odd about them: specifically, that they contain are no instances of ‘000’, and only two instances of ‘111’.
I therefore wondered whether the ‘.’ and ‘x’ character be standing in for ‘000’ or ‘0000’, and ‘111’ or ‘1111’? I converted various permutations for line  (the longest binary-like line) into the corresponding streams of pure binary digits, and then ran them through index of coincidence tests online.
However, I don’t have a positive result yet (the IoC probably isn’t the most reliable test for this kind of thing, but I thought it was worth a try), but if you happen to be looking at this part of the ciphertext, I think this currently seems like the most likely route to an answer.
The Letter Ciphers
According to Cipher Mysteries commenter Thomas, “Conant and B.H. Ketelle were members of the Manhattan Project. Janossy was a Hungarian nuclear physicist at the same time. Tywood is a professor of Nuclear Physics in Isaac Asimov’s short story ‘The Red Queen’s Race’ from 1949.”
Indeed, Asimov describes Elmer (Pop) Tywood in his short story as “Ph.D., Sc.D., Fellow of This and Honorary That, one-time youthful participant of the original Manhattan Project, and now full Professor of Nuclear Physics.”
Unfortunately, “Elmer Tywood was dead. He lay next to the table; his face congested, nearly black. No radiation effect. No external force of any sort. The doctor said apoplexy. […] In Elmer Tywood’s office safe were found two puzzling items: i.e. twenty foolscap sheets of apparent mathematics, and a bound folio in a foreign language which turned out to be Greek, the subject matter, on translation, turning out to be chemistry.”
Mysterious deaths and Manhattan Project physicists were therefore at the forefront of Paul Rubin’s mind: my suspicion is therefore that Rubin’s book of words that would drive his code project may well turn out to be a list of names of members of his imaginary Brooklyn Astrophysics Society. We’ll probably never see it, of course: but it is what it is.