The biggest challenge when studying on your own is having the discipline to carve out the necessary time. Can you commit to several hours every night and at least one full day per weekend? Kill your TV if you have to. Disconnect your internet when you study. Implement a SDN moratorium until after you take the MCAT. This place is a huge time-sink. I studied literally every single night and weekend day for 2.5 months with only 1 weekend off to go skiing (but I brought books with me and studied in my hotel).
As far as how I studied, I purchased a 2005 edition of the Kaplan materials for like $7.00 after shipping from Amazon marketplace and read through the whole thing (ignoring the alkenes and alkynes chapters, which are no longer tested). I made an annotated outline of about 6 double-sided pages while reading. This took me about a month. I got my hands on as many practice materials as I could and did loads of problems and at least a few VR passages if not a whole VR test (from a used EK 101 passages book) each night during the process.
I listened to a used copy of Audio Osmosis in my car on the way to work and home. I put it on my MP3 player and listened to it at other times too. Each time I finished a chapter on my outline I would listen to the corresponding AO segment and make notes of anything I didn't fully understand. I reviewed everything I wasn't comfortable with by turning to more detailed textbooks. Previous editions of college textbooks are dirt cheap, often only $2 or $3 (a great way to save money in college, FYI, because they change so little between editions).
Plan to finish your content review a month before you take the MCAT so you can work on problem areas and take practice tests. I purchased some of the AAMC tests online and some used paper copies. The paper copies (although out of date), provide you with 50% more questions so you can easily pare them down to be the right length for a practice test and have additional material for generalized practice. Get a copy of the current topics outline from AAMC and you will know which questions to ignore. It is very important to realize that the MCAT is a test of thinking, not of knowing. You need to get as much practice as possible taking tests to get a feel for the reasoning required by the real deal. Don't get hung up on content review at the expense of practice.
How you take practice tests is important. Use timed conditions and meticulously review every problem including the correct ones after you finish. You can also re-take the test before you review the questions and look up all the answers. Just make sure that you are learning why you missed the ones you did so you can fix the problem.
The bottom line is that you can definitely study on your own, it just takes discipline.