You may wish to stop to consider what exactly you're trying to do here for a moment.
First off if you're looking to just make a more generalized set of rules like a guide for more formal fights, general village workings, bijuu crap etc, then forget about the whole 'storyline' thing and line out what exactly you plan to put into it. If its to be an uniform thing anybody can check out, think about what a new person could ask about and have trouble with, not what's currently pissing you off personally, and try put its contents in sensible order.
If its instead meant to be a storyline, history or whatever you wish to call it, forget about the rules and get a new name like general SL history or some such. SL is far from perfect canon, it has same roots but it includes a whole lot of filler and non-naruto elements as well, no matter whether one likes it or not, so the 'official' route is not going to work. Needless to say even if you don't want to exclude anyone, to try nail down one and only "official" history, saying this is the one and only true thing that happened, is exactly that; you're basically saying only you are right, nobody else counts, even if you try word it nicely.
For storyline what you'll want to do, is include ONLY the details everyone can agree on. For example, origin of chakra; shinju happens, fruit eaten by kaguya, goes nuts, sealed by her kids, they spread chakra out into the world. Simple enough.
And then you'll leave the rest open, excludes nobody and leaves things far richer than trying to iron out every goddamn detail. For example the al-kahtar from suna? It's not canon so people can ignore it if they so wish, but if they do wish to acknowledge it then it opens an entire new historical period for people that predates even kaguya's arrival.
Short and simple? Make just a base for people, say here's what we know for certain happened, and anything not on here is up to your own interpretation. Its kind of like giving people the base game, and letting them pick their own expansions to it.