Hoo boy, lots of stuff to cover here. First off, I don't think the manifold on this engine clogs up as much as previous models, or the TDI. Mine went 80,000 miles before being cleaned by the dealer (gawd know what they did) and never took a performance hit. Even right after the cleaning, I didn't notice a difference at all. So it may be nothing to worry about.
On the oil mist providing lubrication, that sounds like they are trying to come up with something to convince you to leave the CCV in place, but only because the government requires it. But again, the CCV on this engine seems to have a much better oil separator than other engines. I cleaned the intercooler on the TDI at 50K miles and it made a noticeable difference. But the E300 seems to be running fine still at 100K miles without touching it. So I would say the CCV is not a big problem either.
Now back to the EGR. If you really really want it disabled, then there might be an electronic solution. On the
TDI Club board they describe a device (Epsilonian or eps) that wires in with the MAF and the EGR to fool the computer into thinking the EGR is working. What the computer is looking for is a corresponding change in flow across the MAF when it commands the EGR to open or close, because air is coming from the exhaust instead of the outside.
Now, the question is whether or not the eps will work on the MB, and to my knowledge nobody has tried. There is a replacement MAF that people (including me) are using on their TDI's that is actually a part for a Mercedes CDI engine. So I'm thinking if the MB part works in the TDI engine, then maybe the TDI eps device will work on the MB. Of course the OM606 is not a CDI, but the part looks physically similar. You'd just have to investigate the wiring.