Obsolete/archaic letters in citations

Brian, the issue  here is actually not a citation issue, but a transcription issue. When we transcribe documents from past centuries, we encounter many letter forms that were penned differently than the way we pen then today. Those handwritten letters were also formed differently than the typed characters we use today. To put this into perspective, take your name Brian and write it in cursive. Then type your name. Do you attempt, on a keyboard, to replicate every letter of your name just as it appears in the cursive? No. 

Transcription is not an exercise in copying letter forms exactly. Would you look at an early record about a certain southern state and transcribe the state's name as Mippippippi? Would you read the name "Jesse" and transcribe it as Jeppe, just because the penmanship style of that era used a long-tail 's'?  The same applies to the handwriting of the place and time in which you are working.  "Ye" is "The." The alleged y is actually the thorn character that represented the letters "th." Etc. An 's' is an 's', regardless of whether it is written as a long-tailed character, a rounded s as in most cursive handwriting, or as a double-curve s typically written when we print.

Your issue is both complicated and simplified by the fact that you are not using the original records. Rather, you are citing a book. All that is needed here is a simple book citation.Within that citation, however, you are also trying to deal with two issues that have no role in the citation.

• You are trying to replicate certain letters from the book but not all letters. The form of the letters is irrelevant to the citation, given that Lyndia Henbery's name is written in a perfectly clear fashion.
• You are also trying to add to the citation the data that the source provides. However, a reference note is not the place to include a transcription of the data in the record.That data belongs in the text or narrative or research report that you are writing. If you are at this point simply entering data into a relational database, you are entering the "fact" (or assertion) into a data field and certainly should transcribe the data from the book--but that would be done in the window for "exact text" (or whatever your programm terms it). The transcription of the record does not go in your citation.

All your citation needs to say is something like this:

Albert C. Bates, transcriber, Simsbury, Connecticut, Births, Marriages and Deaths: Transcribed from the Town Records (Hartford, Connecticut: Case, Lockwood and Brainard Co., 1898), 14, for Lydia Henbery's death; citing Deed Book 1 (unpaginated), entry dated 2 August 1689.

If you want to include the fact that you used a digital image of the book online, then the second layer of your citation would say:

; digital image, The Hathi Trust (https://catalog.hathitrust.org/Record/008726049 : viewed 14 August 2016), imaged from original at Yale University.

Brian, you also raise the issue of quoting and how the obsolete letter forms would be rendered in your quote:

While this particular quote is understandable, it made me wonder a few things for quoting archaic language in general.  (The issue might come up in quoting a publication title, newspaper article, snippets from published works etc.)

If I want to make a quote clear for modern readers, is it appropriate to deal with it like a foreign language (which it is, in a way)?

• “Lydia henbery daughter to Aurther Henbery dyed Auguſt ye ſecond Annoq 1689” [Lydia Henbery, daughter of Arthur Henbery died August 2, 1689]

The same principle applies. Quoting is not an exercise in replicating archaic letter forms. You are quoting a set of words and you render those words in modern form. If you are handcopying the quote it will look quite differently than it would if you were typing that quote here on the screen. That's because, in the copying process, you simply use the letter form appropriate to the medium in which you are presenting the quote. In this case, your quote would read:

"Lydia henbery daughter to Aurther Henbery dyed August the second Annoq 1689"

You also wrote:

If I want to eliminate individual arcaic letters (the long s here), is better to show the substitution using editorial brackets, or just make a silent substitution within the quotes?

• "Lydia henbery daughter to Aurther Henbery dyed Augu[s]t ye [s]econd Annoq 1689"

The reality is that when you copy, you are making a letter-form "substition" for every character that you write or type. Even in a typed format, any given word you type in Tempus Sans will  differ radically from the way the letter forms look when typed in, say Constantia. Would you feel the need to use brackets to indicate you are substituting a font different from what was used in the source you're quoting from? 

In the passage above, the only word that might need a bracketed explanation for an inexperienced reader would be the nonstandard (by today's usage) abbreviation of the Latin word annoque.  I.e.

"Lydia henbery daughter to Aurther Henbery dyed August ye second Annoq [year] 1689"