How to structure IDs for new stuff?

1. Yes, must be all unique when working with tuning. The only times when something has the same instance (not tuning ID) is usually for stuff like build/buy or CAS resources to connect them.
2. There is I think, but can't remember the details. The people I do know of who can answer that don't visit the forums, but are in my creator help server linked in my signature if you're extremely curious (and would like to engage with other modders).
3. Tutorial on how to make unique files: www.patreon.com/posts/how-to-start-38023976
Best practice is always created by using CreatorName:ModName_FileName_AnyExtraInfo. You can also always switch it around, but as long as it has your creator name, mod name, file name, and extra details to make it unique you should be good with never conflicting. My current method is MizoreYukii:FileType_ModName_BaseFileName_ExtraInfoForThatFile