There is a section in the map like two similar escalators between Mitsuki's Route and Ayumi's Route. The top one CANNOT be unlocked before you complete the Otherworld Chapter.

After you complete the Otherworld Chapter, you will have 99% map completion if you have already cleared other routes. Follow the route below to get 100% map completion.

Dataload → Start with Best Equipment → Start Game

===Coastline===
Move to Outside my House

===Outside my House===
Move to Living Room

===Living Room===
Move to My Room

===My Room===
Desk x2
Look Around x2
Wall Storage x1
Desk x2
Documents
Don't read the documents
Phone
Clock
Phone
Move to Outside my House

===Outside my House===
Move to School Gate

===School Gate===
Move to Main Hall

===Main Hall===
Move to School Infirmary

===School Infirmary===
Move to Main Hall

===Main Hall===
Move to Corridor

===Corridor===
Move to Labrotory

===Labrotory===
Talk to Yuuki x2
Move to Corridor

===Corridor===
Move to School Gate

===School Gate===
Move to Coastline

===Coastline===
Talk to Toyotomi x4
Move to Shrine

===Shrine===
Talk to Mio x2
Twin Bouldersx2
Talk to Mio x2
Move to Coastline

===Coastline===
Move to Outside my House

===Outside my House===
Move to Living Room

===Living Room===
Move to Outside Father's Study
Door (handle)

===Father's Study===
talk to Ayumi x5
Move to Living Room

===Living Room===
Move to Outside my House

===Outside my House===
Move to School Gate

===School Gate===
Move to Main Hall

===Main Hall===
Move to School Gate

===School Gate===
Move to Outside my House

===Outside my House===
Move to Coastline

===Coastline===
Move to Outside Company Building

===Outside Company Building===
Move to Coastline

===Coastline===
Move to School Gate

===School Gate===
Talk to Yuuki x4
Move to Main Hall

===Main Hall===
Move to School Infirmary

===School Infirmary===
Talk to Eriko x4


You should unlock this tricky route now.

Translated by PDA, you can map each symbol to its corresponding number.
Each number corresponds to the connected blocks in each line.
If one line has more than one number, there should be blanks between these numbers of blocks.

So that we have solutions as below.

You need to push 6 o'clock and 3 o'clock in Father's Study in order to get a jewel.
The hint actually is hidden in the opening move. (These two buttons will shine and thus unlocking the clock)

This one is straightforward. Just follow the translation of PDA.

Thanks for reading and happy 100%!
Feel free to comment if there is any problems.