Here is a step by step walkthrough in 100% completing the puzzle/game.

Puzzle Start

You should click yes when Layton asks his question otherwise. You won't be able to proceed.

Puzzle 1 Answer: B

Town

Click on the wooden menu near the cafe for a hidden puzzle.

Puzzle 2 Answer: D

Click on the barrels for another hidden puzzle.

Puzzle 3 Answer: 1

Get alert that 3 puzzles are complete, can move to Shopping District if you wish, otherwise skip ahead.

Click left arrow to go to the square.

Square

Talk to the lady for new puzzle.

Puzzle 4 Answer: Knight

Click on the bench.

Puzzle 5 Answer: D

Click the left arrow to go to the Housing District.

Housing District

Click on the cat for another puzzle.

Puzzle 6 Answer: 3

Click on the big street lamp.

Puzzle 7 Answer: 2

Click on the left arrow to the Shopping District.

Shopping District

Puzzle 8 Answer: Going clockwise starting at 1. 3, 6, 4, 2, 5.

Click the woman.

Puzzle 9 Answer: 90

Click right arrow to the Housing District.

Housing District

Click on Layton.

Click the right arrow 2x to the Town.

Click the down arrow to Outer Town.

Outer Town

Click suspicious man.

Puzzle 10 Answer: 735.

Click the rock.

Puzzle 11 Answer: D

Click the old lady.

Puzzle 13 Answer: C

Click the flag.

Puzzle 12 Answer: Tailor.

Click up and right to go to the Shopping District.

Click up to enter the Workshop

Workshop

Click the clock.

Puzzle 14 Answer: 3:45

Click the cat for puzzle and rune.

Puzzle 15 Answer: 44

Click the man.

Click down and get an alert.

Click Left to get to the Town and Up to Central Town.

Central Town

Click Layton.

Click Bus Stop Sign for another puzzle.

Puzzle 16 Answer: A.

Click Up to go to forest.

Forest

Click the flower.

Puzzle 18 Answer: B

Click down x2 and left to get to the square.

Square

Click the boy and get rune/puzzle

Puzzle 19 Answer: A

Click right to go to the town.

Town

Click the young girl for another puzzle/rune

Puzzle 20 Answer: 25.

Click up 1x to go to central town

Central Town

Click on the girl for another puzzle/rune

Puzzle 21 Answer: 0

Click up 2x to the temple.

Temple

Have interaction with man.

Click bushes, (only will appear if you have spoken to the hidden man twice, otherwise he won't appear.

Puzzle 17 Answer: 30.

Click on the Temple Doors

Puzzle 22 Answer: Runes at the bottom going from left to right. Put them into the correct colour. Blue, blue, red, blue, red, blue.