I had the same #$%* happen this winter after a motor rebuild, carbs were rebuilt as well. Mechanic said it doesn't like cold starts and runs rough till it warms up, turned out to need the points adjusted as well as a carb sync and mixture adjusted. It was lean as well as not even close to being in sync, I went back and confronted the owner and tech. They offered to make it right, I just did it myself. In my case the carbs were pulled apart and cleaned with all new gaskets and orings put in, the tech didn't even sync it...
It's not like I don't know how to work on my bike, I didn't have the time to do it. Gutting my basement was taking all my spare time not to mention working full time, in the end I made the time and did it myself. Runs like a top now, starts up quick cold and runs smooth. Pulls hard in gear now and does not sound like a twin, sounds like an inline 4 again...
Do it yourself, and know it was done right.