Mike would be a good one to comment but with a more free flowing air filter and exhaust, with the stock needles the bike is possibly running too lean at idle.
I can't comment on why the carbs go out of sync but balancing them is something I do annually (easy 15 minute job with a Morgan Carbtune or similar) and there is always a small amount of adjustment required, afterwards the reduction in vibration is noticeable. So with the bike suffering from excessive vibrations and the hunting issues I'd have to agree with slappy that a carb balance would be a good place to start.