There are small light and dark dots or stray marks all over this letter, just a few on page 1, but definitely on pages 2 to 4. They appear as a single dot on the line, or a dot above the line, or a pair of dots one above the other like a colon.
I think it is going to be difficult to make progress on decoding the dots in the letter page images without higher resolution scans, so I asked Adam on Facebook to provide them if possible. This would be good to mention in today's chat as well.
On page 1, Abby writes "Who I am will possibly be answere(d) in time." This might mean some future time, but it also might be a hint that an encoded message will tell us more about who Abby is.
In chat today, Maddison said she thought the stray dots and marks were just bleed-through from a the marker used to write the letter ... so that's one less code to worry about!