Tuner and Timer, interesting suggestion and great write-up (are you the author or are you passing it along? because it does look familiar!)! SDL, Unfortunately it does not apply to your car or engine! For OM603.961 engine info search for commentary from psfred or gsxr, both these individuals have both knowledge and experience with respect to these six cylinder engines.
You would be well advised to obtain the relevant technical info i.e. the MB engine manual or the CD which inclues this manual before delving into the intricate and precise fuel injection systems. You will at the very least need to know the torque specs for any parts you remove, replace or adjust.
As an aside before you jump into IP timing play have you checked and eliminated the simpler possible problems like EGR, Air recirculation, turbo bearing seal leakage. The question that might be asked is how would the timing have changed enough over a short period to produce the apparent effect? The timing chain is unlikely to strech so much so quickly? the IP should not have rotated out of position easily? Have your injectors been "Lubro Moly Diesel Purged" lately, fuel and air filters changed out? How's your crankcase oil consumption, i. e. is the smoking the product of incomplete combustion or exhaust fouling?
I own the same car so I'll be watching to see how you resolve your problem and what the final diagnosis/problem is, Good Luck!