No offense...but it seems like your car has a new problem every week. Perhaps you need to take it a little easier. More upkeep, less dragracing?
To answer your question, the only time MBZ advises against shifting the car manualy, is when a lower gear is used to slow the car down. This information is in your owners manual.
'90 300SE 298k
-300K and it gets put into retirement.
'80 300D 255k Purchased new by family in 1980.
1973 220 (gas)