For example, when I leave the Imp. City, often Lake Rumare is a dry lake bed and Fanacasecul isn't there.
That could be just the game engine giving you a hiccup. I quite often can't see the water there as well and I'm not even using RAEVWD. It's not the most efficient game engine, sometimes things don't get rendered when they're supposed to.
Maybe clean-up isn't the right word, but I have found that if I remove a texture pack, those textures are still present even if I re-run TES4LODGen. Which directory should I delete if I want to make sure that the most recent run of the generator only has LOD information based on my current mods?
TES4LODGen has nothing to do with textures. All it does is look through your mesh folder for any _far.nif files and adds the information of those locations to the game's data by creating a series of files. You'll find all that info in a special folder somewhere in your Data folder. I forget where it is now and I don't currently have one, so I can't figure out where you'd find it or what's called. The name should be fairly self-explanatory though. You can simply delete the entire folder, TES4LODGen will create a brand new one next time you run it, and the game itself doesn't keep any info there. It normally looks in one of the BSA archives for it.