The alphabetic sequences in the first "cipher" may simply be key material: you can speed up your work by constructing a look-up table that maps each letter of the alphabet to a list of suitable numbers for words starting with that letter.
While encoding is a work in progress this is a perfectly good tool to use, but it is dangerous to explicitly write the letter i.e. "A: 107, 204, ... B: 48, 87, ..." (I made up the numbers) because if the lookup table is found with the ciphertext, the attacker no longer needs to find the correct book (DoI)!
An alternative to actually writing down the letters on the same piece of paper is to have a second strip of paper, to be held above/below the numbers, in an aligned fashion, so that one paper has "A [whitespaces] B [whitespaces] C ..." and the second has some numbers corresponding to the letters. (if you look at things like "indenture" the concept of aligning paper was a commonly used trick for verification etc purpouses)
The grass is always greener on the other side:
1) whenever the encoder was working without lookup table, he labouriously had to traverse the DoI lookinng for a suitable word, wishing he had a lookup table
2) whenever the encoder retried constructing a good lookup table, he (erroneously?) felt he was wasting his time constructing a lookup table instead of encoding the text
this could explain the restarting runs of the alphabet (with letters recurring i.e. aaaabbbccc..., and also explains why the number distribution is flatter compared to N and E as in "Where are the N and E characters" at http://rogergrambihler.tripod.com/BealeHoax.htm )