I think I understand what you've said, but in future, can you break up your paragraphs a bit? You have a lot of ideas and it might help to get them across better. Still, let me clarify something that I myself only discovered a week or so ago:
The plots of the anime (which includes the movies), the manga and the game series are all significantly different, but the games normally share more of these ideas with the manga, rather than the anime (with the exception of Yellow, which was directly based on the anime). For that reason, it's poor form to mix and match elements of both, so I'm more inclined to go with the manga's version of events which show Jirachi underground in the artisan cave.
As for your other ideas, I really like the thought of having secret bases behind waterfalls and underground. That's a really cool idea, and a nice touch. Once I get around to those (it'll be a while) remind me, and I'll try to work them in.
I don't really get the team rocket in Artisan Cave part. They were never in Hoenn (ignoring the anime, of course), and anyone could easily avoid the cave anyway. Although thinking about it, it would be a way to start off the event for Jirachi. I might change it to Aqua/Magma.
Thanks for continuing interest in this, everyone! If you want to show your support, just stick the same LustrousEmerald banner that I have in my signature into yours. I'll post it in the OP as well as updating the plots. I still haven't come up with a good one for Jirachi, so I'm open to suggestions. Yes, he is staying in Artisan Cave, and that's my final decision :D