Sova, before you get ready to add a mod into the MODS folder delete anything but the data folder for that mod. Document folders won't always cause problems, but they could cause SH5 to crash when you install them with JSGME. Readme and txt files that are inside the mod under the data folder should always be removed. They can and will cause SH5 to crash. You can rename them if you want so you can reread the info for that mod, or delete them.
An idea, you might already do this or not, for saving your downloaded mods:
Use only 7Zip for mods. Extract the mod from the zipfile to your desktop, then add it to the MODS folder from there, minus anything but the data folder. All the documentation info will still be saved within the zipfile.
Make a folder for your mod zipfiles you want to save and put them in there. You won't have to redownload the mods again. Even save them to a CD or DVD for future use.
Enjoy.