HOME Menu edits are not the same thing as custom themes; they require significantly more setup/knowledge to create. If you just want to install or create a theme, see Anemone3DS.
This page will cover how to edit the 3DS HOME Menu. By following this guide, you will be able to:
Replace text and words on your HOME Menu
Customize the positions of things like the wireless indicator bar and the time/date display
Edit your Sleep Mode screen completely
Change the color of applets and the words that appear when you open them
Color offsets for these files are different, they are the same for each file;
Color 1
Color 2
0x00001D7C
0x00001D80
After editing all of your files and replacing all the colors, close HxD
Section VI: Editing the HUD
Launch Cheat Engine from wherever you downloaded or installed it
Open the file /ExtractedRomFS/hud.LZ in Cheat Engine
If an error occurs, just press Okay and continue
You may now edit the color and position values of elements as you please
Colors here are not in hexadecimal format, they are in RGB format
Refer to the below image for coordinates;
If you want to remove an element, you can edit the position values of the corresponding element to a very high number
This does not work for the connection status bar. If you want to remove it, open hud.LZ in HxD and change the following offsets to 00:
0x000097E2
0x000098A2
0x00009962
The above are 1 size offsets, so only edit the pair your cursor jumps to when entering the offset value
When you are done editing the values, check the box of each one you edited and close Cheat Engine
Section VII: Using LayeredFS to Apply your Changes
Launch the Home Menu Rebuilding Tool.bat file from where you extracted it if it is not already open and press 6
Navigate to the luma folder on your SD card
Create a folder named titles if it doesn't already exist
Go into your newly created folder and create another folder with the name corresponding to your region;
USA: 0004003000008F02
EUR: 0004003000009802
JPN: 0004003000008202
Copy your ExtractedRomFS folder from where you extracted the Home Menu Rebuilding Tool to the /luma/titles/<name according to region above> folder
Rename the ExtractedRomFS folder you just copied to romfs
Put your SD card into your console
Power on your console while holding SELECT to bring up the Luma Configuration menu
Use the D-Pad to scroll down to Enable game patching and press A to enable it if it is not already enabled
Press START
You should now see your changes when your console boots. Keep all the files in the Home Menu Rebuilding Tool folder in case you want to make more edits later. If you do want to make edits later, start this guide from Section II step 7 and only press 5.
Credits
Thank you to anyone who has helped improve or perfect this guide.