1-2
The two Black Phantom Knights before the Tower Knight area sometimes won't appear. It looks like they will spawn if you go to the top of the tower with the Compound Short Bow treasure, before proceeding to the Tower Knight area. They will also spawn if you do this when backtracking from the Tower Knight Archstone, and then return.
5-1
There should be a third Black Phantom Depraved One as well, but he dies before I can get there no matter how I approach him, from either Archstone. You suddenly get an influx of Souls when you get near his location, equal to the amount you get from killing the knife wielding black phantom. His soul-flame is then found on the bridge between the Rats and the Crystal Lizard, usually containing two Crescent Grasses or a Dark Moon Grass. Doesn't matter if the bridge is up or down, he still dies.