Matt vs. Japan on YouTube talks about how, even after achieving a high level in Japanese, he had to go back and retrain himself to hear and correctly use pitch accent.
His experience won't be 1:1 with what you're working on, but it definitely seems like the last bit of polish in any language will require some deliberate study.
The rough map might be --
Get specific, objective feedback to isolate your biggest problem areas (it seems like you already have a sense of these),
Maybe pick one area to focus on at a time, (depending on how complicated that thing is),
Get lots of input and pay extra attention to how natives deal with that,
Use flash cards to drill on those concepts. For prepositions, say, find good sentences from native language content (books, blogs, movies, TV) that feature prepositions you have trouble with.
For pronouncing plurals you're just going to have to practice pronouncing them in a lot of sentences. In front of a mirror if not in conversations.
Some language learners recommend "shadowing" when you're at an advanced level, that might help with this. It's basically finding someone where you can copy their speech patterns, like a podcaster or comedian, where you can try to mimic and use phrases they say as much as possible to sound more and more natural.
Keep in mind that articles in particular are incredibly difficult to explain in a simple set of rules. It even varies with things of the same type. We go to "the Rockies" and "the Grand Canyon" but just "Pike's Peak" and "Mount Everest." I don't think any English speaker consults a set of methodical rules before using them, and I'm not sure many of us could explain them to you. There are some good rough guidlines out there, but it's going to be a bit like learning genders in other languages -- you just have to learn them as part of the nouns. More input, and mimicking sentences you know are correct, is going to build the instinctive pattern-matching to make this subconscious, like the way English speakers use it.
Good luck, you're at a level not a lot of people make it too. Remember to congratulate yourself for how far you've come while also knowing you can always do a little more.