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Yes, You have to challenge and beat the Elite Four before you can get Rotom
Correct me if I'm wrong, but I think you have to get the national Dex first before the swarms start to happen?
Either way nothing will happen until after you beat the E4
Hope that helped
With Shaymin in your party you go talk to a girl in Floaroma Town & She gives it to you, but only with Shaymin.
When you give Shaymin the flower it will turn into Skymin & turn back at night.
It's a key item, you can use it more then once