Don't get me wrong, EK's 1001 series is good practice for brushing up on fundamental concepts that might be preventing you from getting good scores. I used it myself for Organic Chemistry and Biology, and they were good. But they're not exactly the highest yield practice since they are not MCAT format.
TPR's science workbook is very useful for the next step, though. Most of the questions in that workbook are passage-based, but still test specific concepts. One way you could study for the MCAT is to take your diag, determine which subjects you're weak in, review these subjects, find the passages in the workbook corresponding to these subjects (there is a table of contents listing the topics and their corresponding passages) and work them out & read the answer explanations. That's one way to eliminate your weaknesses and turn them into strengths. Do this after every AAMC CBT you take, using the diagnostic report given at the end of each exam.
Berkeley Review's books are probably the next step; they have MCAT-style passages at the end of each section; so each subject set (two books each) has roughly 800-1000 problems total with answer explanations. Those are great and I recommend it all to everyone in my opinion.
EK's 1001 series for Chem/Physics/Organic Chem are useful for learning the basics, but they aren't in MCAT format and within each section, there are repeats of questions (which is why they tell you to do every 3 questions). So to do all of them isn't that efficient unless you identify which sections you're having trouble with in the corresponding EK subject manual. It's all about efficiency; if you have the time to churn through all 1001 questions in these books, then go for it. But not everyone has the time and willpower to do it.
Bottom line, study smart and maximize the time (and attention span?) that you have in limited quantities.