All stray beads are sorted by location and number. I would highly recommend not searching for stray beads until you've reached the end of the game, as many of them require you to come back for them after getting a brush technique, dojo technique, or advancing the story.

#001 - Southeast of the bridge in the Cave of Nagi, behind a tree and down a small hill in the background.

#002 - In a chest underneath the lookout platform, on the rafters.
#003 - Buried on an island in the northeast section, next to a clover. Easier to find at night.
#004 - In a chest at the top of the waterfall.

#005 - Buried by two trees on a ledge near the shore of the lake, at the base of the ramp to the Moon Cave.
#006 - Buried behind the Dojo, at the cliff between 2 fences.
#007 - Buried around bushes on a ledge on the east side of the river, across from the Guardian Sapling.
#008 - Buried in the north corner, behind Nameless Man's kiln.
#009 - Given to you by Tama after showing him the Cherry Bomb 2 and 3 upgrades.
#010 - Given to you by the Nameless Man after all five of his vases have been offered to the Guardian Statues around Shinshu Field. Only available after taking Lika to Wawku Shrine.

#011 - Buried on the far side of the tunnel, past the fire and near the first tree on the left.

#012 - In the middle chest in Madame Fawn's house.
#013 - Buried behind Karude's house.
#014 - Buried in a ledge close to the cracked wall, to the left of the Tsuta Ruins entra.ce
#015 - Sitting by itself on a tree branch, underneath a Konohana blossom.
#016 - In a chest on top of the tree near the spring on the northwest corner of the map.
#017 - In the middle burning chest outside Madame Fawn's house.

#018 - On a platform after the second tree trunk ramp, in the room where you fight Blockhead. Bomb the cracked wall and use bloom on the bud.
#019 - Behind the cracked wall behind the waterfall where you destroyed the poison urns. After purifying the water, jump down into the lake immediately below and swim into the waterfall, where you'll find a little alcove that has a pot in it. Behind the pot is a cracked wall that hides a room with a bud. Bloom it to get the bead.
#020 - In the long hall where the rolling glass orb was, look for a Konohana flower to use vine on, then bloom the bud.

#021 - In the pond on the right, near the stairs in the tunnel where you fight Waka for the second time. Power slash the bubbles and the bead will float to the surface.
#022 - Buried behind a rock behind Mr. and Mrs. Cutter's house.
#023 - Buried near Bingo.
#024 - Buried in a pile of leaves near the Mermaid spring.
#025 - In the burning chest in the tunnel near the exit to the upper area.
#026 - In the middle chest under the digging spot near Bingo.

#027 - Buried by the bridge near the pond, to the left of Princess Fuse's house.
#028 - Buried inside Mr. Bamboo's house.
#029 - In a chest on the rafters past the banners. Use Galestorm to lift up the banners and jump across them to get to the platform.

#030 - Buried next to the bamboo fountain at the entrance.
#031 - Inside the first upstairs room to the left. Paint a dot on the white eye of the Daruma doll.
#032 - Buried in a chest in a grove at the back of the Bamboo Forest.

#033 - Without getting on the elevator, draw a Cherry Bomb inside it to send it upwards. Then drop into the hole beneath it for the bead and some treasure.
#034 - The burning chest on the 2nd floor.
#035 - Head down the right tunnel from the room with the pool of water to find Princess Fuse training the 8 Canine Warriors. Beat them in a battle for the bead. Only available after defeating Ninetails.

#036 - Bured at the far end of a river bank, past the waterfall.
#037 - In a burning chest near the waterfall.
#038 - Purify all the cursed areas on the other side of the bridge to reveal a chest containing the bead.
#039 - On top of a stone pillar near the end of the river downstream. To reach it, you need to vine across all of the high-flying Konohana blossoms.
#040 - Buried on a small island upstream. Only available after defeating Ninetails and getting the Water Tablet from the Emperor. You will drown if you try to swim, and Water Lilies will be pushed downstream.

#041 - In a chest on top of the Sunken Ship.
#042 - Clear the Devil Gate near the entrance to Sei'an City to reveal a group of rabbits. One of the rabbits is black and white. Carry this rabbit to the Animal Lover (guy searching for his lost pet) over on the beach.
#043 - Buried under a hard rock near the Dojo.
#044 - Complete the Devil Gate Trial Cave in this area. The entrance is a hard digging spot near some cows, behind Ankoku Temple and on the way to the Guardian Sapling. For the gate to appear, you have to defeat the Bandit Spider that lives here, then exit/re-enter the cave.
#045 - Beat Hayate three times in the Racing minigame. Only available after defeating Ninetails.

#046 - In a chest in the southwest section of the canal. If you've restored the water already, use power slash to open the chest.
#047 - Buried behind a hidden wall in Mr. Flower's house.

The next three require side quests to complete. Long explanations ahead.

#048 - At the shop near the Origin Mirror, buy Charcoal. Give this Charcoal to a girl in the east part of town who is drawing some designs on the groound. Speak to her again and pay close attention to the design in her thought bubble. Head over to the Kimono Shop and draw the same design until Mr. Chic accepts it by saying "That pattern almost seems as if it could make something happen". then return to the girl for 20 praise and another design. After successfully drawing 5 designs for Mr. Chic, the girl will give you the bead. *IMPORTANT* The fifth design is always the same, and it is the kanji character for "Heaven"(天). The game is very finicky about this design and seems to only consistently accept it if you use the correct stroke order, which is as follows:
1. Draw the topmost horizontal line first.
2. Draw the second horizontal line.
3. Draw a curved vertical line going to the left, starting from the top horizontal line.
4. Draw a diagonal line going to the right from the second horizontal line.

#049 - Complete a series of racing minigames against Hayazo, and return the four stolen items he drops to their owners. NOTE: You can only do this after defeating Ninetales. It requires knowing Power Slash, Watersprout, Inferno and Thunderstorm.
Glass Watch - Return this to Samurai Dandy, the man in blue near the shops.
Millet Dumplings - Take these to Momotaro, who is next to Camille and Camellia in the day time.
Chrysanthemum Hairpin - Take this to the man in Yama's Restaurant.
Tao Mask - The soldier looking for his missing mask at the Tao Trooper HQ

#050 - Bring Camille and Camellia from Kamiki Village, where you can find them underneath the big Konohana tree by going AROUND the torii (archway) instead of through it. In Kamiki, talk to them and headbutt Camille when she says "If someone would just hit me..." and they will move along to Sei'an City, near the Kimono Shop. Talk to them again until Camilla says "Maybe if trees appeared right here out of nowhere, well...", then paint a dot on the ground to make a tree sprout up. Talk to them again, and then after Camille says "Maybe if there was rain right after the tree appeared...", make a tree then use Deluge before it disappears. After this, talk to her to get stray bead #050. You obtain Deluge by returning to Himiko's Palace after defeating Ninetails, and talking to the handmaiden attending to Himiko's grave.

#051 - Buried next to the small bridge.
#052 - Talk to Komuso and defeat the monsters that appear within 30 seconds. For him to be here, you first need to talk to him in Kamiki Village and Kusa Village and defeat the monsters there within 12 and 25 seconds respectively.
#053 - In a submerged chest to the eastern side of the giant bridge.
#054 - At the dead end outside and left of Himiko's Palace.
#055 - Behind the elevator in Himiko's Palace.
#056 - Inside the electrical box in Gen's Tower. After defeating Ninetails and bringing Gen the Gimmick Gear (obtained by beating all 3 of Ida's races in Shinshu Field) or having the Thunder Edge Glaive equipped.

#053, #054 and #055 require you to defeat Blight and learn Veil of Mist first.

#057 - In an alcove in the hallway on the upperside of the ship. After filling the ship with water to gain access to the other side.
#058 - In the room where you find the Lucky Mallet.

#059 - Buried in the garden in front of the Emperor.

#060 - Buried to the left of the broken stairs near Watcher's Cape.
#061 - Buried near the cows and Yoichi on the eastern side.
#062 - Buried on the west island with the dock and the fisherman.
#063 - The middle chest in the Divine Spring near Yoichi. Requires Digging Champ.
#064 - In the Rocky Area accessible via Mist Warp. You must purchase the Mist Warp technique from the Emperor with Demon Fangs.
#065 - After clearing the Devil Gate Trial Cave on the middle of the western islands.
#066 - Given to you by Urashima after giving him the Treasure Box from the Dragon Palace.

#065 and #066 are only available after defeating Ninetails.

#067 - On one of the platforms on the way up the tower.
#068 - At the top of the staircase, when climbing the tower a second time.
#069 - On one of the small towers at the base of Catcall Tower.

#070 - In the Divine Spring behind the staircase.
#071 - On the top drum in the Mermaid Spring room. You need to use restoration on the third drum.
#072 - Inside a clam in the Water Dragon's garden.
#073 - Given to you by Otohime. After defeating Ninetales, come back and talk to her until she tells you that she is pregnant.

#074 - Buried outside the Dojo.
#075 - At the end of the bear cave, near the path leading to Wep'keer.
#076 - On the icewaterfall next to the portal to Wep'keer.
#077 - Buried near the Mermaid Spring, hidden by a Devil Gate.
#078 - In the Divine Spring you find after defeating Blockhead Grande.
#079 - Appears after you clear the Devil Gate Trial Cave. As you go up the path to Wep'keer, look over the edge until you find a hard-dig spot with a clover. The entrance to the cave is through here. Only available after defeating Lechku & Nechku.

#080 - Buried near the storks by the lake.
#081 - In an alcove with a bear, in the middle of the village near the snowy waterfall.
#082 - Buried near the sheep next to Kai's house.
#083 - Buried in the back of the snowball playground.

#084 - Found on the eastern most platform. Cross the lake to get to the platform, then use Vine to get to it. The bead is in the chest on the left in a block of ice.
#085 - Buried on the cliffside behind Tuskle's hut. Use Vine to get it.
#086 - Buried in the hard-dig spot on the cliffside behind Tuskle's hut.
#087 - In the Rocky Area accessible via Mist Warp.

#088 - Near the end of the second section.
#089 - At the end of the wrong path at the end of the third section.
#090 - After defeating Lechku & Nechku, come back to Yoshpet to face Kai in a racing minigame. Beat her for the stray bead.

#091 - On a lilypad near the Origin Mirror. Use Vine to get to it.
#092 - In a chest on a lilypad in the northwest area.
#093 - Given by Ishaku when you come back and talk to him. You can come back after taking Lika to Wawku Shrine.

#094 - At the top of the hill, after the snowballs.
#095 - At the end of the wrong path near the end of the second section.
#096 - On the landing of the right wall of the Catwalk section. The chest is not visible until you get much closer.

#097 - Buried under the left cannon in the entrance hall.
#098 - On an alcove on the way back from the blizzard machine, on the right, reached by freezing a Flame Spider at its highest position.
#099 - On the outside of the elevator shaft. Freeze a Flame Spider on its middle position to reach a small alcove above the walkway.

Only after learning Blizzard.

#100 - Given to you automatically upon defeating Yami and watching the ending cutscenes.

Lucky you! You're all done.