Hey guys, I decided to try out a 100% run. This guide is based on SLCRG's 100% All Hint Coins run mixed with the Any% route and a few adjustments.
Once again, I use the very simplistic style for this guide, just to make it easier for myself to write it... xD This also means, that it is very likely, that there is a faster route, because I haven't had the time to check every riddles timing and when it is available and if it gets into the Riddle Hut.
I only included the starting and end point of timing, since I feel, that everyone should choose their preferred points of splitting.
Best of luck,
Geshode
TIME START with clicking OK on the naming screen
Prologue
001: Top left city
talk to man
002: Click 1
talk to man, click on barrel (next to door), up
Chapter 1
talk to boy
004: Centre house (with blue roof)
click on clock
005: Enter 34
right, talk to man
006: (A) Put 3 and 3, go to (B) (B) If even, go to (C) (B) If tilt, go to (D) (C) Split 2 left, go to (E) (D) Split 2 of 3 and drop third, take bot 2 to high, drop 1 from low, go to (E) (E) If even, dropped is answer (E) If tilt, high is answer
up, talk to man
007: 2W; 1W; 2W; 1W; 2C; 1W1C; 2C; 1W; 2W; 1W; 2W
click on bush
008: Enter 50
up, click on door
009:
click book case
010: mark 知 (top right)
up, talk to man with glasses (in the back)
011: Enter 10
click on chandelier
110:
talk to woman
Chapter 2
2x down, click on cat, down, click on boat
013: Enter 13
down, click on blue door, click on chairs
014: Click E
click candle
015: Enter 3
down, left, click on cat, click on town hall door, click on bottom glass of right window
118: Enter 1000
click on door, down (twice), click on door, talk to woman (give item to Layton), click on picture above woman
112:
2x down, click on car
019:
right, up, left, talk to woman,
022:
click on sign
111: Mark D
up, click on jar
026: Enter 59
click on cat, talk to man with glasses and beard
028:
talk to man in the middle, talk to man with glasses and beard, up, talk to woman
Chapter 3
click on picture (right side), down, talk to woman, down, talk to man, down, click on cat, 2x down, talk to man, click blue door, click jars on counter
032: Enter 100
click candle
033(give item to Layton): Mark the match
down, left, talk to left man
035: Enter 3
click on left doorway
107: Mark right village (red roofs)
up, right, up, talk to man, 2x down, talk to man
038: Mark Beverages (Top)
2x down, left, click on door, talk to man behind bar
Chapter 4
right, talk to man, left, up, talk to man
046(give item to Luke):
down, right, down, click on sign of hotel
113:
click on door, up, talk to man
047(give item to Luke): Mark B
click on door to Riddle Hut
058:
click on door to Riddle Hut, talk to woman, click on door
003: Click A
016: Enter 7
017: Mark ジェリア
018(give item to Layton):
020:
021: Enter 8
023: 8 -> 5 ; 5 ->3 ; 3 ->8 ; 5 ->3 ; 8 ->5 ; 5 ->3 ; 3 -> 8
024: 10 -> 7 ; 7 -> 3 ; 3 -> 10 ; 7 -> 3 ; 3 -> 10 ; 7 -> 3 ; 10 -> 7 ; 7 -> 3 ; 3 ->10
025:
027:
029: Enter 1
030: Mark house (bottom left)
031: Enter 1
036: Enter 1
037: Enter 6:6
039: Mark hat (top right)
040: Enter 44
041: Click D
042: Enter 95
043(give item to Luke): Enter 0
044:
leave menu (もどる in bottom right), down, 2x up, click on door, click on bottle
106: Enter 1
talk to man behind bar, down, right, click on door, talk to man, click on ham above man
114:
click on door, 2x down, talk to woman
055(give item to Luke): Enter 1
down, talk to man
056(give item to Luke): Enter 2
up, right, talk to man
059:
2x up, click on door, up (twice), talk to man on the left
061(give item to Layton:
talk to man on the left again
103(give item to Layton):
3x down, talk to man
Chapter 5
up, click on door, talk to man, 3x down, talk to woman, up, talk to man, up, click on cat
060: Click ひだり
click on door, 2x up, click on journal (left side on desk), down, talk to woman
063(give item to Layton): Move the hands on both eyes of the woman
talk to man in the middle
062: Mark シゲオ (left name)
2x down, talk to woman, 2x down, left, click on right (blue) door, talk to man,
064: Enter 1
click on door, talk to boy
034: Enter 12
talk to left man
057(give item to Luke): Click D
click on door to Riddle Hut, click on door
012:
045: Enter コンパス
048: Enter 5
049(give item to Luke): Enter M
050(give item to Layton): Enter F
051: Click A
052:
053(give item to Luke): Click C
054: Click the moon
Leave menu (もどる in bottom right), down, up, talk to girl
066: 1 and 2
click on cat/mouse
065: Enter ヒト
talk to girl
067: Enter だいすき
up, talk to man, right, talk to man (twice)
068: Enter 12
click door, talk to man
069(give item to Luke): Enter 29
click door, up, left
070:
talk to man
071(give item to Layton): Click C
click on pillar (Top Left)
101: Enter 6
click on newspaper, talk to left man, click on bookcase
108: Enter み
click on desk, click on right drawer, click on door, 2x down, click on door, talk to woman, down
Chapter 6
up, talk to right boy
072(give item to Luke): Enter 4
up, click on right door, talk to man
109 (give item to Layton):
click door, up, left, talk to woman
074: Click A (the box below the letter)
talk to woman again
075(give item to Luke): Enter 4
up, click on sign (top of screen)
119:
up, talk to woman
102: Enter 20
click on right window (without bars)
117: Enter 1
up, 6x back, left, talk to man
076: Enter 20
talk to girl
077(give item to Layton): Click B
click on door, talk to man behind bar
078(give item to Layton): 16 -> 9 ; 9 -> 7 ; 7 -> 16 ; 9 -> 7 ; 16 -> 9 ; 9 -> 7 ; 7 -> 16 ; 9 -> 7 ; 16 -> 9 ; 9 -> 7 ; 7 -> 16 ; 9-> 7 ; 16 -> 9 ; 9 -> 7 ; 7 -> 16
talk to man behind bar again
079:
talk to man at table
080(give item to Layton):
talk to man at table again
081:
talk to man at table again
082(give item to Layton):
talk to man at table again
083:
click on door, up, click on sign
Chapter 7
down, right, click on blue door, talk to man (twice),
073(give item to Layton): Enter 11
click on door, left, down the hole in the ground, talk to man, click hole above ladder
120:
left, talk to man
084: Enter 3
up, click car
085(give item to Layton): Enter 60
left, back, right, talk to man
086: Enter 4
up, click on poster, up, click on right side of right stand
115: Mark D
right, click on ferris wheel
087: Enter 42
right, back, talk to man
088(give item to Luke): Enter みず
click right part of the building
116: Enter 51
up, left, down, click on tablet in the back
089(give item to Layton):
left, click door
090:
up, click on picture in the back/middle, click on picture on the right
091(give item to Layton): Click B
back, right, up, back, left, 2x back
Chapter 8
go down through the hole, go right, talk to man
092:
back, up through hole, right, back, click on door, talk to woman, back, up, right, up, talk to man
093: S, N, W, S, C, N, S
put picture together (mini game), up, click door, up
Choose the third option: あまーいスイートポテト
Choose the first option: ネコのクローディア探しのとき
4x back, left, 2x up, right, click on door, talk to man
104(give item to Layton):
check rooms (mini game), click door, up, left, 2x up, talk to woman
105: Enter 6
up
Chapter 9
up, click on door, left, click on lock
094:
left, click on lock
095:
up, talk to man
096: Enter 64
left, click on lock
097:
http://layton-fushigi.g-takumi.com/images/nazo/097-3jpg 
right, talk to woman
098: ♦ J ♥ ♣ ♠
up, click on door
099: 41286-7953
click on door, click on lock
100:
2x right, put the robot dog together and give him a name(mini game), click door
Choose the first option: このまま、最上階の家の中に進む
Click on where the apple is supposed to be
TIME END with second text box after last mystery screen
