The only things that count towards the completion percentage are the actual Tasks you accomplish as you progress through the linear storyline, and Journal Entries, many of which you unlock as you progress through the story, but a few of which you have to look for.

29% is divided between the 16 Journal Entries
20% is from completing the Plains of Epheroth
19% is from completing Deilen Fel
32% is from completing Mt. Eldur.
Note that the races don't count towards completion percentage of the save file.

There are 6 journal entries to unlock in the Plains.
- Begin: Unlocked at the beginning of the game
- Missing: Unlocked by interacting with the Voyager flag near where you start the game. (You may have to interact multiple times to cycle through the dialogues)
- Free: Unlocked by collecting all 5 Feathers
- Dangerous: Unlocked by getting near to one of the animals on the Plains.
- Leafy: Unlocked by getting near to the small grove of Purple Willows with the Grass Deer. (Or another tree that's harder to describe)
- Sacrifice: Unlocked by interacting with the plaque in front of the statue of the Alicorn, Tayrin at the end of the Vault.

Before leaving the level, your completion percentage should be 32%

There are 5 journal entries to unlock in Deilen Fel.
- Arrival: Unlocked when you load the level
- Gus: Unlocked by speaking to Gus (The mushroom guy down below)

- Lyari: Unlocked by collecting 4 Feathers
- Teamwork: Unlocked by completing the Sun and Moon game
- Protective Stuff: Unlocked by collecting 7 Feathers

Before leaving the level, your completion percentage should be 61%

There are 5 journal entries to unlock on Mt. Eldur.
- Mt. Eldur: Unlocked when the level loads.
- Dragons: Unlocked when you collect 3 Feathers.
- Jairia: Unlocked when you collect 8 Feathers.
- Conant: Unlocked automatically during the level progression (After planting the seeds).
- Aska: Unlocked automatically during the level progression (After interacting with the pillar with Maximus Vice on it in the Garden of Aska)

Before leaving the level, your completion percentage should now be 100%

As the developer of this game, I can see in hindsight that despite a desire to encourage people to explore and interact with various things, the way in which some of the journal entries (especially in the Plains) are hidden from the player is more frustrating than it is motivating.
I hope that this guide will help to overcome some of that for those who really want to see that 100% save-file.
Thank you for taking the time to play the game, and I hope you enjoyed it!