On peer disconnect, Multiplayer.PeerID should reference the object(s)** to be destroyed.
When a game starts and you have your own variables stored locally or from some ajax, you can simply set those values and relay them through the host with the other players. When a new player joins, it should request those values from the host.
The current multiplayer mechanics are geared toward web based hosts and peers.
The signalling server in the store is for a dedicated hosting of server that allows the connections between web hosts and peers, not a game host itself.
For MMOs you could look into Ajax and PHP to centralize a player database.
As with point 1, you simply need to add references. Though you synch the peer object, with PeerID, you can pass that peer id to anything you create while creating the players assets.
Player.peerid = 01A0
Hitbox.peerid = 01A0
Sword.peerid = 01A0
Helmet.peerid = 01A0
On peer disconnect
Pick objects with peerid = 01A0 (Multiplayer.PeerID) and destroy.
Voor PvP make them enter a room with max 2 players