Also make sure ignition timing is spot on... if the original points system is still there make sure the gap is right on the money...
I have a Dyna-S in my 550 that the previous owner installed. I assumed he did the timing right when he installed it as the bike did run, pretty well actually after the carbs got all situated. however, he didnt set the timing right, 2/3 were off a few degrees fully advanced. I tweaked it and the "koncking" at idle subsided a noticeable amount.
also...where is the bike idling currently?