I clean (nearly) every mod with SSEEdit when it hasn't been done by the author already. But I keep a backup of the original file, just in case it caused issues. I also re-save it to form version 44 in CK64 if it is still form version 43. I test the mod afterwards as far as possible, before cleaning/editing the next mod. But often CTDs are not caused by dirty esp files or dirty edits, but by faulty meshes or textures. Or like my last case: I got a CTD everytime I tried to enter the new CC Tundra homestead. This was caused by a faulty install of a texture mod with NMM. NMM creates symlinks to the files it installs and one symlink was 0 bytes in size. After copying the correct file, I could enter Tundra homestead.