Hi. I know that you are new, but would you please complete your profile with User CP, showing model/year/location as this is often useful in future posts
First, about your ATF change. Your mechanic was quite right about advising you to change the ATF and the filter - if they have never been changed before. We all know that MB originally said that it was not neccessary - but they changed their mind later after some problems.
So get that filter changed asap, (should have been done at 60k miles) and the ATF will also get partially changed, as the TC cannot be drained on your model of transmission. Get someone who knows they are doing to change the ATF. It must be done properly. Probably needs about 5 liters to do the job.
Read the 'stickies' in the W210 forum for details on this task (they use same 722.6 transmission there)
About the brake issue. Are you sure that you are not just feeling the normal ABS pulsing through the pedal that occurs with sharp braking?
I know that you think that your rear rotors (discs) are not warped - but how do you know this?