When i sequentially numbered the DOI found in the book "the Constitutions of the United States" published in 1820, I found like you, 80% of the letters were correct and 20% of the letters in the Cipher 2 message were incorrect.
I had to shift the numbering of the DOI to the right at various points when numbering the document.
When i dug deeper, I attributed this "right shift" to skipped words when TB copied the DOI to a separate sheet of paper for numbering. It appears he skipped
"Forms" located at 245
"The people he has refused for a long time after" located from 480 to 489
"Officers" located at 625
"Has" located at 668
Once you sequentially number the DOI without including these words, 97% of the letters of the Cipher 2 message will be correct.
In order to reach 100% you need to make word 811 a "Y" and word 1005 an "X" because the DOI doesn't have words starting with X and Y yet TB used words such as countY and eXcavation in the Cipher 2 message.
But you already knew all this.