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My gut instinct is that it can be done, but only if you did strongly in Physics during high school. It's been a while since I wrote the MCAT, but you should remember that half of the Physical Sciences questions, will, in fact, be Inorganic Chemistry questions. Therefore, only 40 or the 80 or so questions are based on Physics, and most of those questions, say 30-35, are preceded by descriptive passages. Because of these reasons, I think Physics is manageable.
However, you should really examine yourself and your strengths and weaknesses. Do you think you will need a lot of time to study for Physics? Obviously, the more time you spend on Physics is less time for you to prepare Organic Chemistry, and Biology.
If you have your heart set on applying after third year, then you will need to write the MCAT immediately after second year. In fact, assuming that you are going into second year in Sept. 2000, you could still register for first year Physics, complete it by April 2001, and write the MCAT in either April 2001, or Aug 2001. Either way, you'd be clear to apply to med school in third year. Otherwise it'll just take you an extra year.
So, I think independant study for the MCAT is possible, but it depends on your strength and motivation. I do think it's a lot easier to have the material taught to you than to learn it yourself; there's going to be times when you scratch your head and think "What's going on here?", and it's always nice if there's a teaching assistant around that you can ask for help.