Be on the lookout for the email. They say up to 3 business days, but it is sometimes under 15 minutes.I called Nintendo's customer support. Got a cool dude named Bruno to help me out. I told him what I wanted and he hooked me up. At the most, I'll have to wait three days for the successful transfer. I don't mind - I can just play MH single player until then .
Once the email arrives, you just login and that's it.
The 3DS and part of the Wii U still has traces of their old ways. So one can only hope that things are better on the NX.TBH the mistake was Nintendo making this process so complicated in the first place. I mean you can backup saves and your account on anything BUT nintendo devices.
At least their apps so far are an improvement in that saved data is stored server side. So you just login and continue playing.
Though backingup data on their devices was easy at first. In that on Wii and 3DS it was a matter of just copy pasting content across SD cards. And Wii U was the only system that allowed for external drives at launch. But with the move to cloud saves, again...one can hope things improve with NX.