Ok I managed to fix it, but it does turn out that Arachnophobia isn't done right as after cleaning with xEdit, it still gives the record override errors. I swapped to the Insects Begone mod and after converting a couple plugins to SSE, it works fine as a substitute.
It mostly turns out I didn't have the latest Papyrus tweaks which were only updated 3 days ago (I don't remember if I just downloaded the wrong version or I just missed the updated version) and after reinstalling papyrus and dyndolod, and regenerating the LODs, it seems to work fine now. Oops