1) Wha...? I don't really understand what you're talking about. If you mean what versions do you need to get all 386, logic says all of them, but I swear I remember somebody saying that XD has all of the version exclusives of the one of the remakes. Or else, all the advanced games are compatible with each other (as are the Pokémon) though on some you need certain requirements before you can get some.
2) Beat Mt. Battle in Coloseum or get an Mystic Ticket downloaded into your FR/LG/E game from a Nintendo Event.
3) Get the Aurora Ticket downloaded into FR/LG/E from a Nintendo event.
4) Once you beat the Elite Four (and have the National Dex, I'd assume), it can be found running around Kanto, like Lati@s in R/S/E or and like in G/S/C. Where you find it is luck, really.
5) Snag a shadow Bayleef on Coloseum, purify, evolve, beat the game, then trade, or else complete the Hoenn Dex (200/200) in Emerald and pick Chikorita as your Johto starter.