ButchDiavolo

When dealing with complex parallax, the first thing to download is Parallax Occlusion Mapping. Download and extract one of the ini's into the actual Steam game folder. I use the balanced one. Next download and install Auto Parallax and place it under Resources in MO2. And of course you will need the latest ENB files (currently v0.488)
Next you have to adjust the settings in enbseries.ini so it looks like this:
EnableTerrainBlending=true
EnableComplexParallax=true
EnableComplexParallaxShadows=true
EnableComplexTerrainParallax=true
EnableComplexTerrainParallaxShadows=true
Now we come to the way I have set parallax mods up, which works best for me. As yet, there is no one-is-all mod, which has all the parallax meshes/ textures, so below is the list that I discovered and use, in order of installation. Tastes vary of course, so you can/ should move the installation around for different looks. Skyrim 202x and Skurkbro's mods are the largest files, so changing them around will significantly change the look in game.
To keep things tidy, I created a new category in MO2 called "Parallax" and put all the parallax mods under there. Also, don't merge the parallax versions of Embers XD, Enhanced Vanilla Trees and Assorted Mesh Collection into the respective main mods! I placed the category under "Post-Processing", so parallax will overwrite the normal mods. Below the list will be some more information.
EDIT: for people reading this later. This list is probably outdated.
Parallax Mesh Patch Collection (Enhanced Vanilla Trees) Parallax Mesh Patch - Enhanced Vanilla Trees Fix (fixes the errors in TexGen) Assorted Mesh Collection - Parallax Better Dirt Cliffs and Alphas Shaders of Solstheim Ash and Moss - Parallax Castle Volkihar Parallax Mesh Resources CC's Fort Dawnguard Reborn Parallax Voeille's Soul Cairn HD Expansion Parallax Rally's Solstheim AIO Parallax Rally's Solstheim Landscapes Complex Parallax Skyrim 202x Fomod 2K Skurkbro's Retexture Project - Winterhold Skurkbro's Retexture Project AIO (2K for all options and fixes) Skurkbro's Retexture Project - Markarth and Dwemer Ruins Skurkbro's Retexture Project - Landscapes (2K, Hotfix and Additional) Simplicity of Snow Parallax Riften of Reverie - 2K + parallax meshes ProjectedDiffuse Patch Hub (for snow shaders, pick which you prefer; I use SRP Landscapes 2k) The Omnibus - Terrain Complex Parallax 2K Parallax Caves Nordic Mountains Parallax option Illustrious Whiterun Wood addition first, then Normal 2k (parallax comes later) Vivid Landscapes - Gildergreen Illustrious Whiterun - Parallax meshes As far as Parallax Mesh Patch goes, you can use the main mod as well, but you will need to remove quite a few files that will cause guaranteed CTDs. If you want to use the main mod, please use this guide by Brentw89 to find the files that need to be deleted. It is written for VR, but the same applies for SE/AE. Another kind soul on Nexus made a list of the offending files, so they are also under this spoiler:
Personally, I don't use the main Parallax Mesh Patch mod and have experienced no issues.
Again personally, I use Simplicity of Snow instead of Better Dynamic Snow (v2). You can use BDS instead. If you want to use SoS, you will have to remove the references to BDS from the STEP Conflict Resolution patches.
After installing these mods, it is wise to re-run TexGen and DynDOLOD. I also re-ran LODGEN, but I am not sure if that is necessary.
So, Wall of Text. But I hope it will help you. If you have any questions, just ask. I might even be able to answer them
 

Thank you guys for the tips!
 
Unfortunately they didn't have any effect.
So I decided to do the tedious thing and unticking all the mods I added since I knew it DID work (up until UIO) and then adding them back in blocks of 3. After adding these blocks of mods, I LOOTed and Wrye Bashed. And of course, the very last one I added back was the culprit... It was a TTW Quest mod called "Point Lookout Reborn". This mod apparently had two different ESM, because I didn't merge but overwritten (DUH me). After "optionalising" one of them, I got the Vaultec Dude head and the menu overlay! YAY! So it wasn't actually a F&LNV issue.
 
Unfortunately I am aware that this was a very specific issue that not many people will have, unless they also use this mod and have two ESM. For others who may not get the main menu overlay: this issue is (I expect) very similar to not hiding BSA's after extracting them and/or setting esm/esp from merged patches to optional! So make sure you check, double-check and even triple-check if you indeed did that.
 
Thank you for the help and I hope this will help someone else in the future.
 
- Moo.