So now you know the PO did fool with stuff. He may have known what he was doing and he may not. With the larger main? Something else needs to be lessened usually. I'd check all the jets.
I don't have any advice really on which jets you should use. Some mechanics do play with this stuff a lot more than I have and they have experience with more than one bike. My only real concern is that what ever is done to one cylinder, the same should be done to the other, carb.
I'll try to post a tutorial for you about the shorting method of balancing the carbs. May be what you need, can't hurt. I'm going to sleep soon though so I'll get to it tomorrow I think.