You have to do it by hand, pretty much, which means going into each dungeon and deleting the leveled creatures and replacing them with non-leveled ones. If you want to replace the leveled items with non-leveled ones, you will have to create a new container for many of the dungeons because they usually use generic leveled containers.
Obviously this is a ridiculous amount of work, which is why I've decided to just build a new world from scratch for my mod instead of "fixing" the existing one.