Navigate to Skyrim Utilities folder and create a new folder called "Wrye Bash"
Manually download the installer into the "Wrye Bash" folder.
Run the installer and point it to your Skyrim game folder.
Make sure the boxes for "Install for Skyrim" and "Standalone" are checked.
Doing this will create a folder titled "Mopy" in the Skyrim directory.
This is the Wrye Bash folder and home to Wrye Bash.exe
Add the .exe to the MO Launcher Menu
Using Wrye Bash:
Launch Wrye Bash from MO
At the bottom of your Load Order you will see a "Bashed Patch, 0.esp", right-click it and select "Rebuild Patch" from the menu.
Only enable "Leveled Lists" (uncheck all other boxes)
(if it prompts you to select patches to merge with a popup, select "Skip". Do NOT deactivate the patches as it tells you to. Just skip...If it didn't prompt you, but you see "Merge Patches" enabled in the Rebuild Patch window disable that now. Merged Patches are better done in TES5edit)
Select "Build Patch"
Wrye Bash will now produce a small log indicating the changes it made to leveled lists and your mods
Upon exiting Wrye Bash you will find the newly created Bashed Patch, 0.esp in your Plugins window and a Bashed Patch 0 mod in your mod list.
If you do not see the Bashed Patch in your mod list: Check the overwrite folder at the bottom of the mod list. Inside you will find the Bashed Patch 0.esp and a Docs folder. Close the overwrite folder, right-click it, and select "Create Mod". Name it Bashed Patch.
Place both of these at the bottom of their respective lists. ALWAYS. ALWAYS AT THE BOTTOM!!! (until you start using SkyProc patchers..which you aren't right now...so ALWAYS AT THE BOTTOM!!!)