So, I transfered from Horde to Alliance and when I logged in, my portal to Boralus wasn’t working, I had the quest to talk to Magni, Wrathion, The king.
Am I just screwed and have to do it all again or?
Every dual-faction quest is actually just two copies of the same quest. When you change a toon’s faction, you haven’t actually done the copy of the quest for that faction, so you gotta do it again.
Your progress hasn’t actually reset; if you were to swap back to Horde, all the quests would still be done and you’d be where you left off.
It’s big dumb, but… it is how it is.
This happens?
High Elf Effect in action already! 
Faction-specific quests don’t transfer over. Given the split nature of BfA you have to do Kul Tiras and the War Campaign from the start. Neutral quests I think should stay completed though.