The problem is that I can't tell you what to merge without knowing if you have made your own merged patch.
This is what I did with my current installation, I'm this fellow I installed all of my mods. Then I used FNVEdit's "Apply Filter to Show Conflict Losers". That shows me which mods .esms and .esps are being overwritten by other mods. Then I manually checked each conflict, and decided what to do. If I needed to solve it (one mod's changes conflict with another mod's changes), I copied the records into a new .esp, and merged the changes the mods made into one single .esp.
My Merged Patch contains ALL conflict solutions. If I were to uninstall a vital mod, I would have to redo my merged patch from scratch. But I won't uninstall any vital mod, I'm sure of what I'm playing with, and by having one single mod I minimize "patches".
You, on the other hand, rely on patches made by other authors. These are fine if the conflict is way too complex to solve by yourself (like there are many scripts or something that conflict). But I would suggest that you look at what each patch does, and if it is basic entry solving then you could merge them all into one new patch, or better yet, make your own patch for your entire installation.
What I suggest is that you:
- Reinstall Interior Lighting Overhaul. You should use the option that is base game and all DLCs. That saves you 4 plugins.
- Reinstall Project Nevada. Like ILO, there's an option for base game + DLCs. That saves you 4 plugins, if not 5 (Gun Runner's Arsenal).
- I don't know what IWS is, but I suppose it also has an option for "base game + DLCs".
It is much easier to do all of this when you are installing one by one, checking what to do as you install mods, as opposed to doing it all in one sitting after you finished installing the entire modlist.
Mine was easy to patch: I don't use any outlandish mods, just some rebalance mods and so on, so I didn't have much to patch.