Well, I fixed it, sortta. VERY sortta. By shuffling files around and rolling back some saves (no idea which one ultimately worked) I've reduced the problem to dragons. So now, everything (seemingly) works as it should. Except specifically dragons (so Flemeth, High Dragon), which are still one-shot. I swear modding issues are always the weirdest lol
I have also been using Slinks S3 Savage, had to reinstall the game and added back each mod, one at a time, in order to track down the mod that was incompatible. I eventually solved it and everything worked as it should. I use it in combination with a creature scaling mod from combat tweak, these two work really well togheter because Slinks gives you op gear, and I found out only the extra enemies were a challange, not the vanilla spawns. With the creature scaling mod the difference between the new spawned tougher enemies and the vanilla was mcuh smaller, so they worked great togheter.
Anyway, I have run into the exact same problem, everything works as it should except high dragons. They die in 2-3 hits, which I would assume means they are spawned as level 1? If you or anyone have a solution to this It would be greatly appreciated. It's not a big issue as there are so few fights being affected, but it really takes away the excitement in those situations. Otherwise it is an excellent imo, especially considering I have played this game so much I pretty much know all the scripted spawns from memory.