I had similar problems in regards to the roughness that was corrected by restarting the engine.
Firstly, when the engine computer discover's a mis-fire within a cylinder, it shuts down fuel to that particular cylinder to protect the catatlytic converter from having raw fuel pass through it.
This happened to my engine at about 110,000 miles. The problem was corrected with:
1) New (OEM) Bosch spark plugs
2) New plug wires
3) New coil ends/boots (cheap).
2006 E350 w/ 155k miles (Daily Driver)
1993 300E 3.2L Sedan w/ close to about 300k miles
2003 E500 Brilliant Silver (Had 217k miles when totalled!)
1989 300E with 289,000 miles (had for <1 yr while in HI)
03 CLK 500 cabrio (Mom's)
2006 C230k (Dad's)
1999 S420 (Mom's/Dad's)
2000 C230k Sport sedans
2001 CLK320 Cabrio (Mom's)
1995 C280 My First Mercedes-Benz... (155k miles. EXCEPTIONAL AUTOMOBILE. Was Very hard to let go of!)