In addition to taking the vacuum from only one carb, remove the choke from the carb that the choke cable is not hooked up to. This will eliminate any chances of the choke vibrating closed.
One of the best tips I got on tuning my dual carbs is to purchase a uni-syn tool. They can be found on eBay for short money and go a long way in obtaining perfect throttle response.
As for the linkage, keep working at it. Do not settle for a "this is good enough" senario. It is critical that the linkage is smooth as silk otherwise it can break on you when you are far from home.
