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Think I figured out how to fix it.
Tried the above mentioned mobi-mobi and epub-mobi reconversion.
I removed books I knew weren't indexing on the Kindle using Calibre, then browsed to the Kindle in Windows File Explorer and found some leftover files referencing those removed books - think they're probably index files. Deleted those and think this may have been the core problem.
Found another post saying that one person found long titles to be problematic, so shortened up any long titles in Calibre.
After that tried adding books around 30 at a time - this time the books appeared more or less instantly in the index and I could add them to collections. Kept repeating this process for only mobi files and PDF files and all seems to have loaded and could assign to collections right away.
Hope this helps anyone else experiencing the problem.
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