you have to look in places where a legendary might live (example: Zapdos=power plant)
to find lugia go to the 4 whirl islands
Latios
Well, I guess you mean "Soul Silver", and the main legendary Pokemon is Lugia, Water/Flying-Type.
the only legendary that you can breed is manaphy. and that will result in a phione.
Moltas: the fire legendary bird Pokemon the second strongest bird Pokemon
You can't breed legendary Pokemon eggs on Pokemon SoulSilver or on any Pokemon game.
over 9000
They will simply gain Exp. You can't breed legendary pokemon.
no
It might depend on the Pokemon, though usually you can face legendary Pokemon again if you beat the Champion.
Whirlpool and if you don't like lots of randome pokemon battles a a few max repels would not hurt
Probably either Mewtwo or Rayquaza.