This should maybe be in the main Ham thread, but anyway.
Obviously SPOILERS for those who don't want to know about staging.
1. He's 9 for about 2 minutes on stage. It's a funny moment for the audience, but other than that you don't really care/realize.
2. I don't think whole show is from Eliza's perspective. Not sure where you got that, care to elaborate? If anything, it's from Burr's POV, but songs switch between characters. For example, if it was from Eliza's POV, Satisfied wouldn't exist as a song. The realization is in the last song, that she is the one who kept his memory alive, despite how much he hurt her, and without her who knows how much we would actually know about Hamilton today. That doesn't make the whole musical from her POV. (unless I missed something and I'm totally wrong, then someone please enlighten me)
3. When the gun goes off, the turn tables are spinning, and one of the female ensemble members is holding the bullet from Burr's gun and aiming it slowly towards Hamilton while he does his monologue. He moves around in this scene, some ensemble/principal members come onstage for different parts (i.e. "Washington is watching from the other side," Chris Jackson appears), but right before he's shot (he aims his pistol at the sky, WAIT!), he's back in position aiming at the sky. He hunches over, two ensemble members mime rowing him across the river via the turn tables. He is back on stage during "Who Lives Who Dies" as a kind of ghost/spirit watching Eliza.