SPOILER ALERT
Hi! So, for the alternate true ending you need to make sure the body you-know-who would use in the main true ending is dead. One of the ways to do that is to give your name to the homunculus when they ask you to make a promise and then agree to give blood. After that try to be good and kind as if you are going for the normal true ending (it’s good idea to trade the shiny memory to hermit so you don’t need to look for extra waters). The true ending should proceed as before, but now instead of finding them in the new body something else will happen. As for the scenes, I’m not sure of the top of my head, but do you have two scenes where Vyn is violent with the knife? If those two are missing there is a section in the guide that tells you how to get those achievements and the scenes.