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I basically did the same thing, but i took 3 years at ucsd to finish. I think the best time, assuming you are finishing next year would be the april mcat. That way most of the mcat knowledge from classes will be done, and also if you don't do well, you still have time to retake in the summer. Good luck, let me know if you have more q's about the whole ucsd transfer thing.
If you feel that you need to finish those courses to be ready, I would recommend taking you MCATs in MAY and preferrably no later than July.
Also, these recommendations are assuming that you will take the MCAT just ONCE. Like the previous poster said, if you take it in April, you'll have the summer. But if you need to be prepared, April may not be a good time for you (especially with school and everything else).