The corpse is on the ground floor, so you would have seen it by now if it was there. I have also experienced it going missing, in my case I believe it wasn't conflicting mods, but that the corpse was sinking into the ground. I realised this because on numerous later playthroughs, when I'd wander through the fort I'd notice the body had sunk most of the way into the ground (in some cases just an arm or leg remaining).
I've seen that happen to corpses a few times, so that may well be the answer. I've checked all of Fort Ash again after seeing your post, even using TCL to look underground, so I guess it's probably fallen into Oblivion by now. :whistling: I was quite close to Fort Ash early in the game but got distracted, I only reached it after a lot of game hours. So that first visit may well have triggered the start of the sinking and by the time I returned it was gone.
Not much I can do about the issue with the body. I don't recall ever having that sort of problem with other mods. Plus, moving the body up off the landscape would remove it from casual view. Not everyone reads the semi-spoilerish part of the readme

I've found the RefId of the amulet on the wiki, I've tried to use player.moveto, but that doesn't work. I guess that means player.additem will be the way to go. Will I also need the note to start the quest? If yes, do you happen to have the RefId of the note handy?