1. Several priority windows are created. When the boss is destroyed, it is removed from the game and all face-up events are destroyed. Then one event resource is turned face-up and added to the chain. All players can respond to it as normal, then it resolves and the next event is turned face-up. Then all Minion resources are removed from the game face-up, and a "New Boss" event is added to the chain. All players can respond to this event, and when it resolves, the new boss and all minions removed from the game earlier enter play, along with any Event cards or ally tokens associated with that boss.
2. Currently, yes. Whether or not something will be added to the comp rules removing this interaction is unknown, but it will destroy the current hero (unless that hero is Immune). Note that this will kill all "forms" of the Reliquary of Souls fight, as modifiers still affect the boss in between boss exchanges, however the modifier will not affect the next boss to enter play. Also note that this may change with future Comprehensive Rules updates.
3. Correct, every single time one of your allies or heroes would take damage, 3 of that damage is prevented.
4. If any Minion ally would leave play for any reason, it is destroyed instead, and any resources that the boss controls cannot be removed by the raiding players. Any other card controlled by the Boss player can be removed as normal (although note that opposing players cannot interact with Events in play), and it will be treated normally. Same thing with the Boss player's hand.
WoW characters:
Jadorel, 70 Night Elf Druid, 44/0/17 spec, Agamaggan server; raiding character.
Sethala, 55 Blood Elf Mage, 5/41/0 spec, Rivendare server; PvP character.