I had a very similar situation with the idle after I installed new primary shaft bushings. I sprayed carb cleaner at the secondary throttle shafts and sure enough, the idle smoothed out. If you read through the history of posts, you will find that the rear throttle plates should seat themselves which requires some play in the secondary shafts. If you put your hand over the airhorn when it is running, does it idle better? If it does, you may have a vacuum leak (other than by the secondary shafts) or you may need more idle fuel.
Because I wasn't using the original carb and had taken a core and rebuilt it to Cliff's specs, I had to open up the idle down channel restriction as well as the idle mixture screw openings using one of Cliff's option settings. It idles the best it ever has. (454 with mild cam)
I didn't see any other details about your vehicle so if you can provide more information on make, engine and the work you've done on it, I'm sure there will be others on the forum that can provide some excellent suggestions.