Sorry, I was out of town on business for a while but now I'm back.
I had my mechanic check out the brakes including the calipers, hub runout, etc., and could find no problems. We've removed and replaced the front and rear rotors (the fronts under warranty) and pads with MBZ parts. The left front rotor runout was .004 in; the right front and both rears were out .002 in each.
So, we're starting from scratch and I must say they are very smooth, at least for now. I am being as careful as city traffic allows with the break-in. My mechanic says he has seen bad rotors back-to-back in the past, as I seemed to have experienced, but I'm keeping my fingers crossed.
Thanks for all the input and advice, everybody.
By the way, I had him install Bilstein Sport struts on the front end (I'm not quite ready to tackle the rear shocks yet--$$$$) and I've picked up a little additional compression travel over the stock struts. For those who have lowered their cars without going to the sport struts then you are indeed missing out. Ride quality seems to be as good as before but I get some extra travel and much less "hobby-horsing" than with the stock struts.
92 300E (Black/Grey interior: wife's car)
94 E320 Wagon (White/Saddle interior, Eibach springs, '96 E420 16 x 7.5 wheels)