I admit that I don't know the answer to why this type of punctuation was used or if it had a specific meaning. V. Van Hyning (formerly of By the People LOC) or LOC Manuscript Division do you have any knowledge of why = was used as punctuation in the 19th c that you could share to illuminate this question?
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I've come across this a few times in the course of my scholarly editing. Sometimes the equal signs seem mostly decorative, some authors use them at the ends of lines where they're quoting direct speech, and some authors use them consistently as a stand in for another form of punctuation, such as a dash. In this case the author seems to use it as a dash, but they also use it underneath superscript letters as in 5th. If it were me I might ignore those superscript ones and interpret the others as dashes, which is what I think you've done. To my knowledge these don't have any specific meaning, it's more of a quirk, like someone dotting their i's with hearts. I'd be curious to hear what LOC Manuscript Division thinks though as these materials are later than my own area of expertise. There might be some link between telegrams and these marks, but I don't think so.
As we've mentioned in the instructions and elsewhere, transcription throws up all sorts of edge cases that we can't anticipate. We're most interested in the words on the pages becoming searchable, and though punctuation is important, it's hard to make rules that anticipate each variation. Scholarly editors from different fields, and indeed from the same fields(!) often come to different conclusions about the best way to transcribe. So, as I often say, try your best! It looks like you've come to a good interpretation here.
Thanks for your enthusiasm!