A lot to read. Welcome to Subsim, I just wish it was under better circumstances.
Firstly (I'll read more and digest later), when you failed to Roll Back Sh3 Commander at some point, it corrupted you file set in the 16km (and probably the 8km) Scene Mod. That copy, original or backed up is now borked.
Commander should always be rolled back BEFORE altering any Modded file sets and you should always do this docked at base before/after a patrol.
Moving forward. You said that you reinstalled SH3+GWX completely and used a backup copy of your save data and everything was fine, even with activated mods. You then add additional mods and the problem returned. Did you roll back Commander? Did you use 'clean' source versions of these additional mods or were they left over form a previous installation.
TBH, I'm 99% sure your issues (black sky & Uber enemies) are a direct result of files becoming corrupted after changing mod sets without rolling back.
You're part way there with your clean installation, just ensure that the non-native (to GWX) mods you are adding are re-downloaded from source and are unaltered.
Edit - If the Steam Install is causing you trouble in file removal, check both the Steam Program files folder & the Steam Apps folder. you will find SH3 files in both. I assume you know that GWX needs to be installed to the Steam Apps folder, as do all other mods.
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