Make sure the path for the profile 'FNV' is correct
If it isn't, correct it and if it is select the profile and click ok
Right click on the list and select 'Uncheck All'
Select 'FalloutNV.esm' and click OK
When it finishes loading, click the gear on the top bar
Change the settings to look like the two on the right, but change to path to where your stuff is installed
IMPORTANT: Make sure the plugins you are about to merge are continuous at the bottom of your load order to avoid errors
Deactivate plugins after merging
Launch Merge Plugins through Mod Organizer
Make sure the path for the profile 'FNV' is correct
If it isn't, correct it and if it is select the profile and click ok
Right click on the list and select 'Uncheck All'
Select 'FalloutNV.esm' and click OK
When it finishes loading, click the gear on the top bar
Change the settings to look like they do in the pictures on the right, but change to path to where your stuff is installed
Re-open Merge Plugins and select every mod from each merge list one list at a time
When the background loader has finished, right click on the first mod from merge (Make sure you don't accidentally select one of the official .esms or master .esms)
Select 'Add to merge' and title the merge whatever you'll recognize for both boxes
Repeat for every other mod from the merge
Once done, head over to the 'Merges' tab
Right click on the merge you just made and select 'Check Plugins for Errors'
Once that has finished click 'Done' (There should be no errors)
Right click on the merge again and select 'Build Merge'
Once the building is complete, you can exit and it should save automatically
NOTE: For this merge, make sure 'Copy General Assets' is un-checked in the 'Integrations' tab. Instead of deactivating the mods in the left pain completely, just move the merged .esps to optional in MO