Gods and Monsters

/way 35.8 54.7 Agents of Order
/way 59.2 26.3 Shadow, Storm, and Stone
/way 49.9 20.4 The Curse and the Silence
/way 62.5 37.7 Age of a Hundred Kings

There seems to be a lot of conflicting information here on when you can get each lore piece. This is mostly likely caused by conflicting PTR and post-release information, and it made the process of finding them a little awkward for me during Stage 3.

Here are my screenshots clarifying locations up to and including Stage 4 (I'll update with Stage 5 when we unlock it):

Rumbles of Thunder

[Stage 1] Unity at a Price
[Stage 1] The Sacred Mount
[Stage 2] Lei Shen
[Stage 2] The Pandaren Problem

Gods and Monsters

[Stage 1] Agents of Order
[Stage 4] The Curse and the Silence
[Stage 4] Shadow, Storm, and Stone
[Stage 6] Age of a Hundred Kings

The Zandalari Prophecy

[Stage 1] Coming of Age
[Stage 1] Shadows of the Loa
[Stage 3] The Dark Prophet Zul
[Stage 5] For Council and King - There are some phasing issues with the Zandalari Warship. Be persistent, you'll have a lucky day where the ship is docked and remains phased in.

From these, I've made this map of all Thunder Isle lore.

I have compiled a list of TomTom waypoints for all three of the Isle of Thunder lore achievements:
Gods and Monsters, Rumbles of Thunder, and The Zandalari Prophecy

Note: You'll need to be in Isle of Thunder when adding these waypoints. For some reason TomTom doesn't recognize Isle of Thunder as a zone.

/way 35.8 54.7 Agents of Order
/way 49.9 20.4 The Curse and The Silence
/way 59.1 26.2 Shadow, Storm, and Stone
/way 62.5 37.7 Age of a Hundred Kings

/way 40.2 40.6 Lei Shen
/way 34.9 65.6 Unity at a Price (inside Hall of the Grand Imperion)
/way 47.0 59.9 The Sacred Mount
/way 60.7 68.8 The Pandaren Problem

/way 35.2 70.1 Coming of Age
/way 36.4 70.3 Shadows of the Loa
/way 68.7 45.8 For Council and King
/way 52.6 41.4 The Dark Prophet Zul