Orgo I & II were absolutely my favorite science classes. I love the combination of memorization and reasoning, the puzzles of synthesis and spectroscopy, and the real-world ramifications of the material. Of all the pre-reqs, they were also the hardest by a good amount...but the pain was worth it. 🙂
As for the MCAT, the Biological Sciences section does have a decent amount of organic. The material is from anywhere throughout the two semesters; in fact, when I took the test last April, one of the passages included a reaction that we covered two weeks later in class. Thankfully, I was able to use everything else to pull together a decent showing in the passage. (So I think, anyway...)
Unless you are unusually dedicated and have access to faculty, you will not be successful studying orgo II out of the EK book! At the very least, you should use a regular textbook and go through the material carefully. I would personally wait until you have taken both semesters of orgo, or are at least mostly through second semester, before taking the MCAT. Otherwise, you are going into the test with the knowledge that you have already given up points.