I have some Haxe coding experience due to the engine, so I can help you with some things.
Song Files
.json files are the type of the file your chart is saved on when you save the chart.
Story Week and Song List
You can change what songs are in which week, and even delete a week altogether. I'll let you try to understand whats going on in both versions of the file.
Freeplay Songlist
This is easy. Just enter your custom song's name with a capital letter at the start of every word. After doing that, you can play it in the Freeplay Menu. It is utilized in every engine, even in the original game.
That's just basic knowledge. Things like Modcharts I can't figure out yet, but I hope this helped by giving you more info about the engine.
When I named my custom song "Chilledwindows" with no spaces, it worked. But when I named the other custom song "Temptation-Before-The-Dawn" (t+pazolite reference) which has dashes (which corespond to spaces ingame) the game either crashes or that weird song glitch happens where the chart just keeps looping every chart beat without the actual song ever playing.
Find the weeklist in the data folder. (it is recommended you find the v2 version) I won't go too in detail on what the file name is or where it exactly is, but you'll know it when you find it.
Delete the instance of code used for the Tutorial Week.
