Here's a simplified guide for tracking down the various +stat crafting items, key materials for BiS weapons and armor, as well as where to find Learning Point Shrines in the world. I'll keep updating this guide as I discover more during my current playthrough.
Learning Point Shrines give +3 Learning Points.
Learning Point Shrine 1
Learning Point Shrine 2
Learning Point Shrine 3
Learning Point Shrine 4
Learning Point Shrine 5
Learning Point Shrine 6
Learning Point Shrine 7
Learning Point Shrine 8
From the 8th Mandragora or Southeastern Root Mother, go west/southwest and look for the semi-hidden path in the water (if you have the detailed map it's MUCH easier to see). The shrine is hidden under trees across the river to the north, verrrry sneaky spot.
Basaltroot gives +1 to strength when consumed raw or +3 when combined with a Mandragora into a potion.
Basaltroot 1
Enter the cave and go Northeast from the entrance.
Basaltroot 2
Enter the cave and keep heading East/Northeast. Eventually you will reach a wall that can be broken. This will bring you inside the tavern cellar basement with all the rats. The Basaltroot will be in the Northeastern corner near a Rock Monster.
Alternatively, you can do the Rats! quest and get here as well.
Basaltroot 3
From the same cave, go south through the water passage and into the mole hole. From there, go east towards the mole by the water. Then, go south past the 4 sleeping rock monsters and head west when the passage forks. The Basaltroot will be in the corner.
Basaltroot 4
From the mole hole in the cellar, follow the passage through the rock worm section and up into the spider nest. Head west through the spider nest and keep destroying webbed passage entrances and you will eventually find a Basaltroot on the floor in the corner. This one can be tricky in the early game due to all the spiders but if you keep dodging and attack the main webs you can stay ahead of them.
Basaltroot 5
Lobo the merchant has one for sale for 200 coins.
Basaltroot 6
Very linear cave, just kill the few moles in here and it's right at the end. You can't miss it.
Void Plant gives +1 Mind when consumed raw or +3 Mind when combined with a Mandragora into a potion.
Void Plant 1
Void Plant 2
Void Plant 3
Void Plant 4
The plant is just south of the border of the Forest Map. From where you fight the spider boss, just head south and it's a little off the edge of the map.
Void Plant 5
Requires Misty Step to access. Near the Sword in the Stone.
Cliff Lichen gives +1 Dexterity when consumed raw or +3 when combined with a Mandragora into a potion.
Cliff Lichen 1
Cliff Lichen 2
Aiden has one for sale for 200 coins.
Cliff Lichen 3
Cliff Lichen 4
Sneaky path hidden in the trees
Cliff Lichen 5
It's a ridiculously wide wrap around. Come in from the south east, wrap around to the north west clockwise, then once you find a big quantity of black flame, go south east through it and look for the trees hidden path. It's hard to explain, this one is a tough one.
Alternatively, come in from the north side via the Bandit ruins entrance west of Remnant Ruins. It's another wide wrap but it's another option.
Cliff Lichen 6
Lobo has one for sale for 200 coins.
Cliff Lichen 7
Where you drop down to get to the Vorago shrine past the lady who gets mad at you for picking Rustroot. Look to your right and look behind the tree, if you just head straight down hugging the wall (like MOST of us do) you will not see the Cliff Lichen because it is barely outside the fog of war. Right click to see these sneaky shenanigans!
Mandragora 1
Mandragora 2
Talk to Jesko, he is selling one for 500 coins.
Mandragora 3 (optional)
This one is part of the "Man in the Moor" quest. Henrik teaches you how to catch Mandragoras and even gives you ear plugs so you don't die. What a nice guy! Let's repay him by not giving him the Mandragora we catch. More Stats vs just XP, you decide.
IF YOU DECIDE TO KEEP THIS MANDRAGORA, YOU ARE LOCKED OUT OF THE NEMETON FACTION. HENRIK CANNOT HELP YOU WITH THE VANISHED WEAPONS QUEST IN ORDER TO JOIN THEM WITHOUT GIVING HIM THE MANDRAGORA.
you can get the Optional Mandragora back if you pull out your weapon and fight him in town after you give it to him. It's a tough fight, but when you win, you can loot him for his gear which includes the Mandragora you gave.
He will be mad at you and you will need to pay 200 to forgive the crime, though.
-HunTurkey
Mandragora 4
Mandragora 5
Mandragora 6
Mandragora 7
Bombus has one in chapter 2+ for 500 coins
Mandragora 8
Signet Stone 1
In Boris' Chest. Sleep til 23hr and Gera will be outside smoking. Creep inside and grab the stone out of the chest.
Signet Stone 2
Talk to Jesko, he is selling one for 1500 coins.
Signet Stone 3
Go into the ruins and do the light up floor tile puzzle to get access to the loot room that has the Signet Stone in it.
Signet Stone 4
Check the 4 corner rooms of the ruin and press the hidden blocks there are bandits looking around for them as well pretty much walking right up to half of the blocks (super obvious, no need for screenshots).
Signet Stone 5
Nothing too crazy, just dodge ghosts, they won't follow.
Signet Stone 6
Just unlock the hatch in the ruin on the plateau.
Complete the "Missing" Quest to receive the Strange Relic which acts as the 7th Signet Stone.
Then, bring them all to the Ruin Raiders and you can buy the Best Weapons in the game as well as an Elixir of Concentration and an Elixir of Life.
When you have 3 pieces, bring them to Bardok or Chunnaic (must be a member of their faction).
Armor Piece 1
Open the hatch on the plateau.
Armor Piece 2 and 3
Push the stone on the wall behind the statue to open the stairs down. Then you need to bring your fully activated key. All Signets found/combined and activated via turning on all 7 shrines. This will open the way to the end of the Ruin's Raiders questline where you will fight 2 golems that hold armor pieces as well as Drivanius for the Nexus Helmet which is used for the good ending of the game.
Armor Piece 4 and 5
Armor pieces 4 and 5 are located in the back of the Hewer Cave in the Remnant Camp. Misty Step across the water and prepare for the hardest fight in the whole game (imo). This fight has 2 golems much like the previous one, but this time, a TON of adds that just won't stop coming. Kill the golems FAST and drop the adds even faster to even have a chance at this one. The second you pick up the Vortex Mask on the table, the door behind you seals you in and all hell breaks loose. Have fun!
Armor Piece 6 and 7
Pieces 6 and 7 are both in the Old Library. The main quest line brings you here, very hard to miss these.
Armor Piece 8
Inside the Spider Temple on the Floodplain Knoll. Part of the main quest line, just make sure to clear out the spider tunnels to find it near the spear. Clear clockwise starting from the west once you get to the main room and work your way around to find it.
Armor Piece 9
Also part of the main quest inside the Forest Primeval Temple ruins. Can't miss this one, you have to fight the Golem to progress.
Step 1
Go here late at night 22-24hr and play the Lyra to the flashing of the fireflies.
Step 2
Engrave this symbol onto the talisman (it appears on the rock near the fireflies)
Blessing 1
Go here and stand inside the circle for a few seconds.
Blessing 2
Just on the island near the Learning Point Shrine.
Blessing 3
Your reward for this pain in the ass is a really solid Talisman that will allow you to equip higher prowess gear much easier.
Missing
Get abducted at either of the 2 black dots if you want to have the "kidnapped" experience.
Or go to the Star and have a"Jailbreak" experience from the outside in.
Either way, this gets you the "Strange Relic" which is the last Signet you need for legendary weapon purchases.
Dreams of Another World
This quest can start wherever Lorthiz is when he has his dreams. I've seen him in Chapter 2 in the Primeval Forest, but most of the time at the Ripper Inn.
Part 1 is the Crazy Lady in the South Moor
Grab the fossil off her body and bring it back to Lorthiz
Part 2 is the Ruins Raiders tunnels. Go Northeast and look for the parent and child skeletons
Part 3 is the starting ruined town hatch that wouldn't open.
Part 4 is in the moor with the lantern in the cave
Enjoy the awesome legendary ring. Multi hard hits are best for recovering HP.
Shrines
Throw these items into the well at the shrines
Sol - Sword
Apus - Ram Figurine
Terra - Lyra
Cygnus - Mirror
Luna - Rustmoss
Vorago - Clam
Bootes - Horn