Step 1 Create your custom route by Tiled.
(1) Create the route map:
(2) Export it to the .lua
Step 2 Convert it to bin
I wrote a lua script for it. Run the script and you will get your bin. Remember to keep the route.lua you got in the previous step in the same folder.
For how to install a lua environment, google it.
Step 3 Open your rom with a hex editor and paste the route.bin to any freespace. Then repoint it.