I’ve been there too, and I have a very similar learning experience with Japanese : high school classes for 3 years, reached the « old »
JLPT 3 level, then self-study through various means. The only difference is I jumped early into reading, and only very recently came to read manga (all my teachers emphasized that reading manga is difficult, and can be counter productive if you don’t already speak Japanese at a relatively high level)
I used to just read as much as I could even if I didn’t understand whole sentences, sometimes whole paragraphs, because stopping to look even one word in a dictionary takes time and breaks the reading flow.
I got better … very slowly….
And then recently I discovered the combo yomitan + ttsu reader !
Basically, ttsu reader is a web-based app that will accept epubs (so you can read novels you care about, and not only websites or made-for-learners text like Satori Reader), and Yomitan (the new version of Yomichan) is a very, very good pop-up dictionary, way better than the kindle dictionary for example, that you can customize to your heart’s content with bilingual dictionaries, monolingual dictionaries, and even grammar dictionaries. It has been a complete game-changer for me, because it’s super fast, so you don’t lose focus on the text when looking something up, it helps with collocations and idiomatic expressions, not just with words, and while I almost never used yomichan/rikaichan/rikaikun/etc for websites before, I use it a lot when reading books.
Compared to other dictionaries, yomitan will also parse the verbs for you, so not only will it give you the translation of the word, but it will also automatically tell you that it is passive/causative/causative-passive/whatever, so it will shed light on those foggy parts, and do it fast.
You can also use it to mine sentences directly into Anki, but even without doing that, it has been a huge help for me.
And if you’re not a fan of reading on you computer, you can also use it on an android ebook reader.
Setup can be a bit bothersome, especially if you try to do some fancy things with Anki, but it was worth it.
As for ttsu-reader, it handles epubs, furigana, vertical reading, has a tracker, and you can set goals for your readings (I try to read 3000-5000 characters a day). And it will sync with your GoogleDrive or OneDrive if you want to use it on several platforms….but will also work offline.
I still have those « foggy » moments when I have no idea what the sentence means and have to re-read it, but now it only happens once every 50 pages or so…
So even though you state in your original post that it’s not a problem of simply looking up things in a dictionary, I think it still is, because you actually need to use several dictionaries and reference books to get the complete meaning of a sentence, and that takes time and break your flow. I find it simply way easier with ttsu-reader paired with Yomitan, and really encourage you to give it a try !