I have 3 questions: 1) I already beat the Elite Four, the first time..

1. Actually, the champion is your rival.

2. You have to give the ruby to Celio found in Mt. Ember. Celio will give you a rainbow pass, having access to all the Sevii Islands except the islands you need to get through a nintendo event (like birth island).

3. You can get the following Johto Pokemon in 3-7 island and in the cerulean cave by catching them:

Sentret, Ledyba, Spinarak, Togepi (you receive it as an egg by talking to a man in Water Labyrinth), Natu, Marill, Hoppip, Yanma, Misdreavus, Unown, Wobbuffet, Dunsparce, Heracross, Slugma, Swinub, Sneasel (LG), Delibird (FR), Remoraid, Mantine, Phanpy, Larvitar, One of the three legendary dogs. You get the other Johto Pokemon by evolving them. Otherwise you have to trade from Pokemon Collesium.

1)You need to beat your rival.
2)Get the Ruby from Mt.Ember and give it to Celio. He will give you the Rainbow Pass for it which enables you to go to islands Four, Five, Six and Seven.
3)You can't get Johto Pokemon in this game normally.

1)First you need to get to four island, which leads us to Q.2.

2)To get to four island, you first need to catch 60 different pokemon. Then you go to Proffesor Oak and he will give you a new pokedex called the National pokedex. Then, you go to one island and talk to Celio. He says that there is a ruby gem that is somewhere on the island but doesn't know where it is. Go to Mt.Ember and once you get there, keep heading right and up until you get to two team rocket grunts guarding a cave. Battle them and go inside. Make sure you have the TM's Strength and Rock Smash. Find your way to the gem and bring it back to Celio. He will give you the Rainbow pass, which means you can access the rest of the islands.
3)I think you have to get the sapphire gem before you can get to some Johto pokemon. But you can find some slugma's in Mt.Ember when you are searching for the ruby gem.

Hope this helps!

You get Khoto Pokemon on island 3 through the cave on island 3's port.