A mess o problems compiling a complicated project

Just converted to Scrivener 3, with a major Scrivener project (130k words using the Non-fiction Format) using both endnotes and footnotes, imported from an older Scrivener version. Questions:

  1. I’m setting the endnotes after each chapter, and want to convert them to an “Essay on Sources”-type format. Is there a way to preserve links to specific pages without cluttering up the manuscript with visible superscript indicators such as 2 or *? Published books with source essays at the end with page headers that say “notes for pages xxx- xxy’ etcetera—is that done usually in the typesetting/printing process, or is it usually the writer’s responsibility to set it up in the formatting? If the latter, how?

a. what’s the difference between an “inspector footnote” and a “linked footnote” which resides in the inspector column? Is this gonna cause glitches in the compiled document, and if so, how do I prevent them?

b. When I transform an inline footnote into an inspector footnote, Scrivener 3 [seems to] transform all inline footnotes in the section, not just the particular one I’m working on. So then I have to go back and do all sorts of workarounds to recreate any footnotes I want to maintain as “real” footnotes (i.e. at the bottom of the page). How do I avoid this problem?

  1. I put a first line indent into every paragraph, but the compile process tends to strip out the indent of the first paragraph of each chapter and of some sections. Any ideas as to why, and how to fix globally?

a. sometimes the text slops over into the (bottom-of page) footnotes. How to find and fix in the scrivener original?

b. Sometimes after compile I get two (count em, 2!) lines with centered pound signs (#) between paragraphs, or between sections (i.e., after the chapter folder but before the next text Subsection). What’s up with that?

c. Occasionally (tho not in pdf??) both bottom-of-page footnotes and endnotes (that is, inspector footnotes) come out doublespaced! “Convert[ing the guilty paragraph] to Default Formatting” (in the Inspector) does not seem to fix the problem. Wassup?

  1. The Scrivener mss text is Calibri (Notes somehow in Sitka small), but parts of the compile (for pdf, rtf or docx) come out sometimes come out in what looks like Calibri, but mostly in what looks like TNR or Courier or whatever! Again, any ideas as to why, and how to fix globally?

Have you looked at our Upgrade Guide? Scrivener 3 completely overhauls the Compile command relative to Scrivener 1. Scrivener 3: A Guide for Scrivener 1 Users | Literature and Latte

Yes. These are problems regardless of the edition: I don’t believe they’re caused by the conversion from one version to the other (I just included that FYI). The problem is that the Scrivener manual is itself so complicated that I can’t find the answers. I need a problem-solving approach.