I'm working on a MED9 1K0907115B.  I occasionally get a few hundred RPM idle bounce with my foot off the clutch, and in neutral.  Typically bounces about 6 or 7 times, and eventually levels out.  Most common situation is slowing to a stop for a light.  Mostly, if not always, after its up to temp. Typically if I hit the clutch, it will go away completely, or stop temporarily.  Doesnt change with hitting the brakes or any other intervention.  Stock dual mass flywheel and clutch. Am I correct in thinking that I'm dealing with idle torque here? KFMRES, KFMRESFS, KFMRESK, KFMRESKNL.  If i'm thinking of the correct revisions of my file (because I've been changing other things as well, and trying to correct this) it did it with stock values, and does it with values I tried that I found in a "big box tuner's" file.  I did notice the stock values are different between some of the maps, and the big box tuner's maps all match.  Should there be a difference between them?  Whats the proper way to go about adjusting these?  I will soon be installing a single mass flywheel and upgraded clutch.  Will these need to be adjusted again afterwards?
Any insight is much appreciated. 

It happens in three different cars, and goes away with a stock file, or a different tune.  Throttle body clean may help, but I doubt its the source of the issue. 

This sounds very similar to when I had a vacuum leak on my S3 as well.