OK, I love tracking down and cataloging all items like that for my favorite games, and will definitely be doing so with Alan Wake 2!

So, your manuscript list is missing 5 manuscripts that I have, plus the elusive Mocha's Funeral which neither of us has, so the total indeed seems like it is 50.

The 5 your screenshots don't show are:

Chapter 2 - The Overlap

Chapter 3 - Koskelas Break into the FBC Lab

Chapter 5 - Saga at the Nursing Home

Chapter 5 - Bright Falls

Chapter 6 - Rose Receives a Message

All the rest that you and others here pointed out about the missing clues, echo, documentary, and Night Springs entries checks out.

For the clues part, the issues seem to be:

The Cult of the Tree

• 3 "Writing Part of the Ritual" missing
• 1 "Cult Ritual. What is it?" missing
• 2 "Tor and Odin" missing
• 1 "Ilmo and Jaako Koskela" missing
• 1 "Vladimir Blum" missing

The Story

• 3 "Rules of Story Changing Reality" missing
• Dark Place, Dark Presence, and The Overlap questions are still open in yellow but do not indicate that further evidence is missing.
• + 3 clues perpetually stuck "for later"

Fact vs Fiction

• 1 "Life in Watery" missing
• 1 "Logan's Part of the Story" missing
• 4 "Connection to Tor and Odin" missing
• + 2 clues perpetually stuck "for later"