You're running two unmodified Rochester B's on an engine that used to run right with only one of them? Of course you're going to have problems. There needs to be some major changes made in main jetting, and power valve calibration. Another option would be to set up your throttle linkage like the Buick and Hudson systems used to use, where only one carb handles idle and low speed to midrange throttle positions, and the second carb opened quickly for full-throttle operation. Hudson called it the "Twin-H" system, and it was used on their racing models, IIRC. Some Buick straight 8's also ran two carbs, with one used for high-speed only.
Jerry