I asssume you have checked that the oil level is right to the top of the fill plug? Have you tried the standard shift lever adjustment with Special tool 9120? It's a real easy dealer adjustment.
I am sorry and I really feel guilty, but mine shifts pretty good, however I have noticed one thing. If you have driven a lot of standards as I have, you have a rythem of clutch/gas that is instinctive, right?
With the stock chipped Xfire the throttle response has a delay which throws off this rythem and you get the jerk! I know it sounds funny but as I got used to the delay, my shifts smoothed right out. Just try to hit your throttle quick and you will see what I am talking about, there is a noticable pause. When I get mine chipped this summer, I'll probably have to get used to the quicker throttle response all over. Have any of you tried the standard shift chipped? Sorry about the spelling!
PS: I saw an article in a magazine about 4 months ago that commented on the MB SLK standard transmission that said that "it is a good thing that MB upgraded the standard trans as the earlier 2000 models were pretty bad". I assume we have that newer model?