I just recently installed the skyrim legendary set and took time to redownload and set up all the mods that I had used before but they don't seem to work anymore. When I uninstalled skyrim legendary and went back to just my regular copy of skyrim the mods still no longer work. I could really use some help figuring out what is causing the problem.

...but they don't seem to work anymore. (You mean they don't showing up under skyrim DATA files ???)

I don't know for sure but if you use SKSE:

SKSE is made for a certain exe file of Skyrim. The legendary edition may not have the same version number and it won't work if it doesn't.

They do show up in the data files and when I even made sure they were checked in the data files when I loaded up the launcher but for some reason they don't seem to work anymore. I had a body replacer, several armor mods, a hair mod, and a few face texture mods but none seem to work when I load up my save file. They did work the day before I installed the skyrim legendary set.

Could you try on a new character ???

I tried several that use alot of these mods and I run into the same problem with each one. I even just tried starting a new save and the mods don't seem to work for that either.

Hmm, you installed legendary edition over the regular skyrim, and then uninstalled the L.E. again.

Should i ask if you want to make a clean skyrim installation ?????

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Uninstall skyrim from Control panel - Program and Features

Next, delete your skyrim folder under C:\Program Files (x86)\Steam\SteamApps\common

Delete the Skyrim directory under C:\Users\[Your name]\Documents\My Games. (Backup your save files if you want)

Then under C:\Users\Poweruser\AppData\Local\Skyrim - Delete that Skyrim folder. (under View - Options - Folder Options - View - Advanced Settings: Show hidden files, folders and drives)

Uninstall any mod manager too: SKSE or NMM

Clean your Registry with Ccleaner: http://www.filehippo.com/download_ccleaner

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After that install L.E edition + DLC's from your stream or from the disk.

DISC INSTALLATION:

Using Steam launch options to install retail games from disc

1. Log in to Steam and click on Library.
2. Right-click on the game, select Delete local content, and confirm.
3. Insert the first disc into your computer.
4. Close Steam (Steam > Exit).
5. Press Windows Key + R to open Run
6. In the Run window type:
   
   "C:\Program Files\Steam\Steam.exe" -install E: or "C:\Program Files (x86)\Steam\Steam.exe" -install E:
   
   Replace E: with the CD/DVD drive you are installing from if is not correct.
   Replace C:\Program Files\Steam if your Steam installation is not in the default location.
7. Press OK. Steam will launch and ask you to sign in if you do not have your password saved. Your installation should continue from the disc.

I just finished trying what you suggested and I am still having problems with my mods not working.