Yes, Tuning plays a huge part in how well the engine runs. Turblown can elaborate on this more, but I know he has done lots of tuning on rx7's, which HATE to idle smoothly, and usually misfire a bit. But if you find the right air/fuel mixture, and set the timing right they will idle sooo smooth.
Syncing carbs can make a huge difference. If they are off, 1 cylinder is firing at 95% and the 100%. Now imagine walking with a bum knee...you dont walk smoothly. Same kinda principal...