You could be dealing with the choke being set too rich. You didn't say if you had an automatic choke or manual. If auto, With the air cleaner off have someone start the car. when it starts and is running rough open the choke approximately half way and observe if the engine smooths out. If it runs better you need to lean your choke setting up. Also if auto choke, does it have a two spade type electrical connections? If so this should be hooked up to allow the choke to go to full open quicker. An overly rich choke will start to fowl the plugs also causing a rough running motor that will go away as the choke opens and the engine clears out.
If this helps check your plugs, you may have fowled one bad enough that it won't clear out and is trash. In this replace the plugs after you get the choke working right.