Hi Francois,
You are a very dedicated language learner! I think you set a high, yet attainable, goal for yourself: being as good at the language as a native speaker. Remember, it takes about 18 years for native speakers of Chinese to reach university level Chinese.
As for stopping flashcards: you can stop using them when you don't really care too much if you remember a new word or not. For example, I'm a native speaker of English. I usually look up 2 - 3 English words per week, but I make no real effort to remember them. It might be years before I encounter those words again, so I make no effort to remember them. However, when I was preparing for the GRE (to get into grad school in the US) I looked up, wrote down, studied, and memorized lots of English words, and did quite well on the verbal section of the exam. I just don't bother with English words anymore, except for the rare word I want to add to my active vocabulary. So I would say maybe when you know the most frequently used 5,000 - 7,000? (8,000?) characters, and the 詞 in which they are used, you will see little additional utility in learning yet another Chinese word. It could be years before you would encounter that word again, and most native speakers will not know that character either.
Here is some further food for thought: I noticed you said you like to read "tough" books, but you can only read a few pages before you need a break. Let me suggest that you try reading "easy" stuff instead. If you read easier material, you will be able to read much, much more. That means you will be exposing yourself to more Chinese. The quantity of material you will be able to read should more than make up for it being "easier." You will see the words you are learning more often because you may be reading 3 or 4 or even 5 times as many pages of "easy" Chinese as you were reading of "tough" Chinese. This, of course, assumes you can find "easier" reading material that interests you.
This method might also help increase your reading speed. Reading speed increases with practice. You need more practice reading. How does one read more? Read easier material!
Cheers,
Bawanglong