Okay, so I can't guarantee that this'll work for you, but I went from a 36th percentile on my first MCAT to my current 82-97th preliminary in CARS by changing my technique (I used to just read the passages the way EK recommended). I realized that I got bored out of my skull and wound up zoning out without realizing it a lot, and I attributed it to being overwhelmed by the length of the passages. When I thought things like "Augh, i'm not even half-way done" that meant I immediately lost focus. So I decided to read the passages in bursts. Divide it mentally into paragraphs (small goals).
I would read the first paragraph, stop, and try to pick out the main idea of the passage when I did this. If it was there, great! If not, I noted what it could be and moved on. Eventually you should be accustomed to finding the authors tone and message. I found that by doing this after every paragraph, I started to connect the paragraphs by which ones helped the overall argument, which ones hindered it, etc. It also helped me remember where various details were more clearly in case the question targeted a specific part of the passage.
I also scribbled brief notes after every paragraph on my scratch paper, but I cannot recommend doing this. It is a time sink, and I only did it because I couldn't get into the habit of stopping to think after every paragraph without it. Overall, I must've spent about 10 minutes per passages (10 minutes/passage * 9 passages = 90 minutes) and barely finished. Of those 10 minutes I spent about 4-4.5 minutes reading it, so my method is highly frowned upon because most people on these forums recommend 7 minutes per passage. The best I can say is try various methods that increase your focus.