Oh well, I was a little concerned changing from Japanese vehicles and purchasing my first German car. With 900 miles, I now have a rough shifting manual and a check engine light...kinda makes me wonder. Everything seems to be running fine so I hope it is a quick, simple fix.
Are there any known issues that commonly happen with the C Class at this mileage?
Hope this isn't an omen of bigger things to come.

bring it to the dealership and let them read that error code.

Well...there's a reason MB only puts a manual transmission in one car..enough said there. If you just came from a Japanese car then your in for a new experience, MB's and German cars in general will have you visiting the service department at least once every two months. Out of all the MB's I've had I have noticed a trend that more and more little problems will start popping up around the 45k - 50k mile range. The good news is everything is under warranty and your only out the time and gas it takes you to get to a service center. By the way...my MB dealership has had far and beyond the best service I've ever had and that includes American, German, and Japanese service departments.

what do you mean by a "rough shifting" manual? is it a clutch issue, is the engine stumbling?

Clutch is great, the 1-2 shift is always rough getting through the gate. It's much better when fully warmed but just takes a lot of patience when cold. As far as Chilledbenz's comments regarding the German cars having little things fall off of them as par for the course; I guess I was hoping the all out effort from Mercedes in addressing exactly that issue would have helped that. And for those of us who have driven manuals a good bit in Europe and Asia, we know that Benz can indeed make a very solid manual transmission...maybe just not the smoothest come to think of it...
Still admit, I am confident this will end up being a solid car, just a little disappointed.

Um, I'm counting myself lucky then. In nearly 15K miles, it's been to the shop for the 1-3K mile checkup, and the 13K service A. Else not.

My old Hondas were similar. Only needed to be in the shop at the service intervals. And they weren't cheap to repair. I'm thinking that labor is just plain expensive

Guess I am lucky as well. Most of the work done on my cars are routine work.

On the e320 - needed a new left cat, but with 180K on originals, that's great. - 182, 980K and going!!!
CLS- Fresh air pump. All else is service A & B 46K on car
R Class - Airmatic Pump, all else service A & B 18k on car

MBz is intended to go for 200,000 - 300,000 miles. Your car hasn't even begun its break-in yet.

Our 4 1/2 year old C240 has had only one failure, the alternator.

My new C350 has been perfect for the first 5,500 miles. I expect it will be even better than the '04

I've really only taken the car's in for service and nothing major under warranty. These newer benz's run like champs.