DanimalTwo

See this post: https://forum.step-project.com/topic/4482-skse-install-detailed-instructions/?p=71594

In your profile folder "MO/profiles/{where ever you call your profile}" edit your SkyrimPrefs.ini and change "bFloatPointRenderTarget=1". By default it is "0". This is needed for ENB.
 

You did not install the aMidianBorn - Content AddOn from AmidianBorn Book of Silence. It is under optional files.

If you installed all those as separate mods, then yes. Copy the asset from the folders from top to bottom in order. For me they are in two mod folders, "RS Children Overhaul" and "RS Children Patches". But installing all those as separate folder is fine too.

Yes.

Hopefully, you deactivated the main mods ESPs by double clicking the mod in the left window, selecting the 'Optional ESPs' tab, and moving all available ESPs to the top optional ESPs. I have the replacement ESP installed in a separate folder which I call "Bathing in Skyrim Merged" and is placed right after "Bathing in Skyrim" in the left window. This contains the new "Bathing in Skyrim - Main.esp". Make sure both these mods are activated in the left pane by checking the box. On the right pane, select the plugins tabs and make sure "Bathing in Skyrim - Main.esp" is activated by checking the box next to it. Hope it helps.

Here how I do it. These instructions assume you know how to use an archive extractor like 7zip (or whatever) and that you know the normal proceedure for installing any other mod using Mod Organizer (MO) in which the DATA folder may not be the top folder.
1. Download SKSE to you MO download directory, just like you would any other mod you wish to install.
2. Using Windows navigate to your MOdownload directory and find the SKSE archive, I use skse_1_07_00.7z.
3. Open the archive with whatever tool you use (7zip, etc.) You will see a directory called "skse_1_07_00", Name maybe different if not using SKSE 1.07alpha.
4. The *.exe and *.dll files in that directory will need to be copied/extracted to your steam skyrim folder (usually "[steam folder]steamappscommonSkyrim"). The files are skse_loader.exe, skse_1_9_32.dll, and skse_steam_loader.dll.
5. Then using MO install the DATA folder as you would any other mod (this is where I assume you know how to do this) and call the mod whatever you like. I use "Skyrim Script Extender".
6. In MO in the left-pane move the SKSE directory to the top of your load order.
7. Using Windows navigate to the SKSE folder and in that folder create a folder named "SKSE". If you are in the right folder before you create this directory you will only see a "scripts" directory.
8. Navigate into the newly created SKSE directory and create a file called "SKSE.ini".
9. Copy and paste the following into the SKSE.ini
10. The [Memory] section is ONLY for SKSE 1.7 alpha. If you do not use that version, do not include that section.
 
I hope that is fairly clear and simple. There really is  no need to create a seperate archive just to install the DATA folder.

The error you are reporting has nothing to do with MO. Let me take a wild guess and assume you are using Bring Out Your Dead (BOYD) version 1.2.3 and Skyproc Unified Manager (SUM). BOYD 1.2.3 assumes you are using an unreleased beta version of unofficial skyrim patch. You can read about it on Neavalen's forum here:
 
https://forum.step-project.com/showthread.php?tid=1392&page=281
 
If my assumption is true the fix is either to revert to BOYD 1.2.2 and rerun SUM or use TES5Edit select SUM, right click on it, and select "sort masters". Best bet, do not use BOYD 1.2.3, it is bugged.