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Alright, so in this tutorial, I'll explain how to merge your leveled lists for EVERY mod in your load order.
The process is very simple, and mostly automated, only requiring your manual input for conflicts that can't be solved on its own.
Depending on the size of your load order, the process could take a few minutes, or about an hour or two.
But, at the end of this tutorial, you'll have every item in containers, vendors, and spawning on NPCs that should be.
First thing's first, the only tool we need is xEdit. If you don't already have it, you can grab it from HERE.
You can extract xEdit anywhere you like, but I recommend putting it somewhere in your Fallout 4 game folder. (I use "Fallout 4\Tools\FO4Edit")
NOTE: After you've extracted the files, you must rename "TES5Edit.exe" to "FO4Edit.exe". This tells the application what game you're running.
Mod Organizer users will need to add the application to its executables. You can do this by hitting the Gears icon at the top. Enter the title "FO4Edit", and hit the "..." button next to "Binary" to browse for the "FO4Edit.exe" file. When everything's set hit "Add". You can now launch the application from the Drop-down list from the top-right. You can also create a shortcut for quick-access. 
Make sure your Load Order is correct, and launch FO4Edit. A window will pop up, with ALL of your plugins selected. This is what we want, so just hit the OK button.
Now, FO4Edit will begin processing all of your plugins. This could take a while, depending on the size of your load order. So, feel free to grab a cup of coffee, or make a sandwich, or watch some cat videos on YouTube.
When it's done though, you'll see all of your plugins listed on the left-side panel, and a message log on the right-side panel. The message log's last entry should say "Background Loader: finished". Once you see that, we're ready to start.
Right-click anywhere in the left-panel with the plugins, and select the "Apply Filter" option.
A window should pop up with many, many options. Don't worry, you can copy the options I have set below:
After you've set those options, you can hit the "Filter" button. Now, we play the waiting game one more time. Back to YouTube for more cat vids. This one will take longer than the first wait.
(You can actually monitor its progress, and make sure it's not frozen by just looking at the window header.)
When it finally finishes, it should show you a few plugins, who all have conflicting leveled list entries.
FO4Edit contains Automatrons that can automatically merge the leveled lists together, and create a single patch for each plugin in conflict here. Cool, huh? Well... It can kinda do that... The feature is still in its early stages, so depending on how many conflicts there are, it might not be able to solve them all automatically. That is where the human touch is needed.
Let's have one of these robots give us a head start, though. We can created the automated patch by Right-clicking anywhere in the left-side panel with the plugins, mousing over "Other" at the bottom of the menu, and using the "Create Merged Patch" option.
(It'll tell you that this is unsupported in Fallout 4, but the Leveled List options are working, at least to the degree that I mentioned previously.)
Hit "Yes" to continue, and it will ask you to choose a name for the patch plugin that you are about to create.
I recommend that you don't get fancy with this, and choose a name that you will remember.
Hit OK, and your automated Leveled List patch will be created! Only... Hold on...
Few caveats here... Hit the Plus Sign (+) next to your leveled list patch. You might notice there's more records in there than we want...
We only wanted the "Leveled Item", "Leveled NPC", and "Leveled Spell" records, but for some reason we've gotten more.
(I'm actually not totally sure why this happens. The FO4Edit tool is still in Beta phase, and probably needs more work in this area.)
Either way, we can remove the records that we don't need by Right-clicking on them, and selecting the "Remove" option. It'll ask you if you're sure. Yes, we are.
Now, we've got only the records that we want, and this is where the human touch comes into play. We've got to double-check that the robot that created our patch, did it correctly. So, let's expand our "Leveled Item" records to take a look.
So, if you don't know much about using xEdit, you're gonna learn some now. :p
(Also, I suggest you read the in-depth documentation HERE if you want to dig deeper than this.)
We're going to focus in the colors here, and I seriously hope you're not colorblind. They tell us the status of the conflicts.
You'll see in my image above, I've got some records with a Yellow background, and Green text.
This means that there is no conflict. Either our robot did it's job well here, or there were no conflicts to begin with. In any case, we don't even need to look at these records, because they're good to go.
You'll also see records with Red backgrounds, and Orange or Brown text.
The Red background means there is a conflict! But, since our new patch plugin is lower in the load order, it will always have priority. The Orange or Brown color means it wins the conflict. Again, our robot did its job here. It automatically created an entry where there was a conflict between 2, or more, other plugins.
(Or, inherited an entry where there was no conflict, and that new entry is being seen as the conflict.)
When you see Orange or Brown text, it means we should take a look. The robot did something here, and we should check its work. For 2 reasons:
First, we need to make sure that the method it used to resolve a conflict is the method we want. It may prioritize one mod's edits over another, and you might want it the other way. Or, in some cases, you may want both.
And second, we have to check that it has actually solved ALL of the conflicts. Sometimes it leaves some unresolved conflicts.
Taking a look at my 10mm Pistol Leveled List, we can see that there were 2 conflicts. (Red background means Conflict, remember?) We can also see that our patch has resolved one of them. (Brown text, see? It's all coming together.) But, the second conflict is still unresolved. Our patch is overwriting it with an empty entry, making that entry null. This is probably the most frequent thing you'll run into.
How do we fix it? That's easy. xEdit kinda works like an Excel spreadsheet, with rows, columns, and cells. So, if you Right-click in the cell, under our Patch's column, for the "Leveled List Entries" row, you can add a new entry.
Boom, you'll see a new entry pop up at the top of our Patch's list. Now, all you need to do is click and drag the information from the conflicted entry into our new entry.
NOTE: You can copy the entire entry by dragging from the top-most column. In this case, I would drag from the conflicted "LVLO - Base Data" cell under my "test - deleveled items.esp", to the newly created "LVLO - Base Data" cell under my "Leveled List Patch.esp". xEdit will prevent you from dropping the information into any other cell, so you can't screw it up. :)
Now, we've resolved all of the conflicts in this record. Notice again that, while the Red backgrounds mean that there is still a conflict, the Brown text under our Patch plugin means that it overrides those conflicts with its own entries. And, we've made sure that those entries are correct. We will continue to check any records with Orange or Brown text from the left-side panel. Make sure that the entries within have conflicts that are resolved properly by our plugin.
I'll give one more example here:
The above image shows a Vendor's leveled list. You can see there is a conflict here. By default, "Fallout4.esm" distributes up to 2 Laser Pistols to this particular level 7 vendor. But, "Weaponsmith Extended 2.esp" decides to change that to 1 pistol. When we create our patch, the plugins lower in the load order have priority (Just like they would in game), so our patch has inherited that conflicting entry from "Weaponsmith Extended 2.esp".
But, you may not want this. You may want the Fallout 4 default behavior. That is something you can decide here, by using your human judgement.
Solving all of the remaining conflicting records can still be a time-consuming process, depending on the size of your load order. But once you've finished, take a sigh of relief, stand up and stretch out a bit, crack your neck. You can save your new Leveled List Patch simply by closing FO4Edit. You'll see a new window pop up with your new plugin and a check mark in it. The check mark means you want to save it. You do, so hit OK.
NOTE: It's worth stating here that, if you'd made any mistakes, or accidentally edited another plugin, REMOVE the check mark from that plugin at this point. You don't want to save those changes.
Once FO4Edit is closed, your new Patch plugin will be saved in your game's "Data" folder. If you use Mod Organizer, the plugin will be in your "overwrite" folder. Make sure the plugin is LAST in your load order, and launch your game. Make sure it loads properly, and you should be seeing all of your items spawning in containers, vendors, and NPCs as they should!
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