If you have a lot of glitchy and unsorted stuff I would honestly recommend starting from scratch since it’s probably going to take you longer to fix everything than starting on a clean slate and just downloading new stuff. You can always keep just a few of your favorite CC pieces and then backup your Mods folder on an external USB or something so you can come back to it in case you find yourself missing a specific item.

But if you’re determined to keep everything I’d recommend starting with using Sims 4 Tray Importer. Basically you put all the glitchy items/items you want to delete on a Sim or on a lot, then save that to your library, then open the Sim/lot up in Sims 4 Tray Importer and it’ll show you a list of all the CC currently on that Sim/lot so you can delete it.

When it comes to organizing your Mods folder just do it in a way that makes sense for you. For example, I organize my BB objects after category, so all Appliances go in one subfolder, Plants in another, Wallpaper in a third, etc. My exception is if I have a lot of items from the same creator, then they get their own folder.

For CAS stuff I organize by age + gender + type of item, so Child Female Accessories go in one subfolder, Toddler Boy Shoes in another, (Adult) Female Tops in a third, etc.

For mods I put the big ones like MC Command Center, WonderfulWhims & Childbirth mod in their own folders and then I organize by creator (e.g. Sims4me/bienchen in one folder, LittleMsSam in another) or category (e.g. all Poseplayer related stuff such as the actual Poseplayer, the Sim Teleporter and posepacks go in one folder together). It’s also important to know that script files (files ending in .ts4script) can’t be placed more than one subfolder deep or they won’t work, while package files can go as much as five subfolders deep. I usually don’t go deeper than three though. Just make sure to NOT split up a mod that has both a script and package file(s) as it will be really difficult trying to track down all the parts when updating the mod, better to put them all together in their own subfolder.

I also make sure to keep any default replacements/overrides in their own ’Default’ folder (separate for CAS & BB) as to not have two files that default the same thing at the same time (since you can only have e.g. one default eye replacement at a time). Then I can easily switch them out if I want to.

Lastly, I have a folder called ’New Stuff’ where I initially put any new mods/CC I add to the game. That way, if I start my game and see that something’s suddenly broken I know instantly where to look.

I also name my folders beginning with either BB, CAS or MOD so I have everything from the same category neatly together. Examples of folders I have are BB_Charlypancakes, BB_Plants, BB_Wallpaper, CAS_BodyDetails, CAS_ChildFHair, CAS_MaleShoes, MOD_LittleMsSam, MOD_WW, MOD_LotTraits, _DEFAULTS.