I ended up retracing my steps and I found the other two parts, Ill attach the locations here that I found them but upon looking at it further im not sure if theyre related to the secret quest. I turned them in to Valyra in the roof of the world hoping they would maybe give some hints but they didnt say anything substantial, although the Ruination of night did seem to give me some good hints I think it was only coincidentally related to the secret quest. @DK_Death I put the locations of the other two here, the quest started for me when I picked up Dirge of Night even though I already had found Ruination of Night, can you take a screenshot of End of Nights text before you turn the quest in? I forgot to take one and it removes the parts from your inventory when you turn the quest in, just in case it is related to the secret quest it would be good to have a screenshot of the third part here.
Those items are just for getting a quest done that gives you +1 skill point, they’re not hidden, but you do need to explore everything 
Got it down when I blitzed through the campaign on release night, until 7am NZ time…
The real secret’s in the fairy rings, the sword and that door in Pilgrim’s Rest that we can’t open, yet.
Yeah I’m definitely thinking its not related now, there was a bit there though where I thought it might be related due to it and the swords both mentioning primordials. @Joneleth was mentioning earlier that they got the potion modifier to see hidden things and the fairy rings were just giving loot drops but didnt seem to be special other than that, but I dont know if they had checked all of them yet or not.
There’s also a Runed Orb hiding up on the Roof of the World that might be involved, as it can’t currently do anything
There’s another mushroom circle in the NW part of the Rotting Croplands, using the potion also reveals a chest in it
This quest turns out skill point reward. I answered “Curiocity” when he asks what did you feel when you read it. I dont think it matters whatever your answer it is tho.
Yeah I tried talking to the orb with the restored Shadowheart in my inventory but it didnt unlock any new dialogue options, the orb might be related but if so we probably have to do something else still first.
There are strange 2 monsters near Frostveil Highlands rift.A deer and a rabit.They got no hp or something and they die from 1 hit but i havent seen any like them anywhere else in the game.Maybe there is some connection?
Thank you for the updates everyone, I have added them to the main post for tracking and added more directions on a few that were missing them.
@Veno, are these mobs the standard ambient mobs that have been added to the new FoA areas?
You’ve probably noticed Elk, Rabbits, Foxes, etc. in your travels through the world. I thought they had health bars though.
Is there anything else unusual about these two?
Are the flower circles maybe related to the new cache achievements? I don’t have enough rep yet to buy the modifier, can anyone who can reveal the treasure confirm if they got an achievement for doing so?
I have but after 12nd spot i obtained not 10 as achievement says.
Just found one of the circles in Frostveil Highlands (don’t know if someone already reported) I’ll try to upload an image
edit:
edit2: it was already on the original post nothing new then xD
After grinding the rep I did all the circles we found I and got the achivement
Hey, read the original post, didn’t (yet) read the entire comment thread, but one thing to add:
That scorched tree in the beginning of FoA is for a regular quest.
Later, one TP before Kurnhold, there is a guy who’s freezing.
By his questline you either choose to freeze him even more, or relief the curse.
That tree is for one of the choices.
(Not that I’m sure it isn’t a part of any other quests, but at least I know this detail).
Thank you, I chose to freeze him so I would not have known about the tree. I will remove it as a contender.
Where is the Mammoth Burial Ground? I dont see it on the GrimTools map or in any of the associated regions. Cant search for it either.
Since its missing from the map and cant be searched, its may be a secret and worth more investigation.