Convention for excerpting from the middle of a paragraph in another work?
I don't do this sort of research, so I can't answer if there is a 'standard approach'.  I have read analytic works on the writings people such as Charles Sanders Peirce, who was notorious for having both a vast and an unorganized body of writing, including personal letters.  Yours might be similar, though in your case it seems even more important to be very precise about what source material you are referencing and quoting.  To my eye, it resembles Biblical analysis in this way.

I like the idea of assigning paragraph numbers to all your source material, but I would suggest using them differently.  In your quotes, I suggest quoting only the relevant words, using ellipses as appropriate to indicate omitted text, and also new lines or paragraph marks to indicate a break in paragraph. But at the end of each quote, in square brackets, you could add the paragraph numbers of the sources, plus any qualifying remarks, such as "spanning both paragraphs" or what ever.

Using your example:


  "... Maecenas mattis erat in metus ..." [citation, starting mid-pargraph in §52 "Lorem ipsum dolor..." and ending mid-pargraph in §55 "...nunc sollicitudin lectus."]


This approach has two advantages. First, your quote includes only the text relevant to your exposition and analysis.  This will make it easier to read and understand.  Second, exact and detailed context information is given in the square brackets following, including the citation if needed.  This will serve you as researcher or a reader who needs to follow along in the source documents.