Didn't go through the whole thread, so if this general advice (which I've learned the hard way) has been said already, I apologize.
MO is an absolutely fantastic tool that enables you to play Skyrim while modding Skyrim: pure gold. Gone are the days of completely screwing up your game and having no idea how to get it working again, and consequently not being able to play, for days or weeks, the game you've been enthralled by, while you figure out what the hell went wrong.
But there are two major pitfalls in the learning curve of MO that can get you back stuck in modding hell if you're not careful:-
1) Overwrite must always be clear, in every profile. That means, soon as something pops up in Overwrite in a profile, make a mod out of it specific to that profile and relevant to whatever spat it out (e.g. FNIS, Bodyslide, etc.)
2) You often need to make several copies of a given mod for the left pane, named appropriately per Profile. For example, weather mods, lighting mods and body mods are usually quite choosy wrt what other mods they play with. That means, if you have only one copy of the mod, the way it's set up in the Profile you first set it up in it might work in that Profile, with the other mods that Profile has, but not in another. So the idea, when this happens, is to be aware of how mods play with each other, and to reinstall and rename COPIES of the more complex mods that have different setup requirements depending on what other mods they're interacting with.
Once you get these two basic rules down pat, the power of MO is yours - you can have umpteen Profiles with umpteen completely different setups, some with a broken Skyrim, and instantly you can go back to the Profile you're playing your main ongoing game that you love, with full confidence that it'll fire up properly and the Profile will be exactly the same as the last time you played it, no matter what else you've been doing in other Profiles. And that means you can test setups in other Profiles, and gradually add the good stuff to your ongoing game, enriching it as you go.