If an auto center only did a front wheel alignment, unfortunately you were ripped off. The vast majority of front wheel drive vehicles, including the Ford Focus, require four wheel alignments. The alignment of the rear tires/wheels can also be adjusted and needs to be in synch with the front tires/wheels. If that isn't done, then a proper alignment wasn't completed.
So did you replace the one tire with the size that didn't match with a matching tire to the other three, I take it?
So you are saying that the car vibrates with the engine running but the car not moving? If this is the case, it's most likely the right upper/passenger side motor mount. I'm not suggesting you just go ahead and replace it, hoping for the best, as that's a great way to waste money. Have the motor mounts diagnosed to determine if the are worn out or not.
-- B.F. Goodrich T/A Certified Tire Specialist