Can you compare the stock idle advance to the advance you currently have? That can often help you smooth things out.
Also use the datalog to grab the information you have, its handy to be able to sit down of an evening with a beer and have a look around at what happened.
Sound advice
There are a few things that could cause a rough idle - you just need to work through the basics.
Are there any airleaks?
Is the base reference angle correct? (so that what you see as ignition timing in MT is the same as you measure with a timing light)
Is the car going to have a lumpy idle? (big cams, lots of overlap)
Is the lambda at idle OK? (should be about lambda= 0.95 to 1.0. any leaner than 1.1 may cause problems)
If the answers are no, yes, no and yes, then take a look at what the ignition advance currently is at idle. You probably want to be in the 10 to 15 BTDC region normally. Any more retarded than about 0 will start to cause problems with combustion, which could cause a lumpy idle.
If you are running very retarded, increase the map values and that should improve things, and also increase the idle speed.
If you are already in the 10 to 15 region then open the throttle a bit with the idle screw to increase the idle speed
I guess for a smallish 4 cylinder you want to be at about 850 - 950rpm at normal warm idle.
If this is all ok then you start to look at more subtle things like plug condition, leads (if you have them), coil dwell time, injector PW (are you on the minimum pulsewidth?), fuel pressure etc etc
