I've been dealing with a P0101 MAF code with rough acceleration and black smoke in the exhaust for the past couple weeks in my 2004 Jetta GLS TDI PD (175,000mi). I've replaced the MAF sensor, changed the fuel filter, patched a hole in the intercooler and checked the intake, exhaust, charge air system and vacuum hoses all reasonably well by eye but the code still comes back after I reset it and drive around 20mi. Also the engine seems loud and there is something like a thumping noise that I can hear really well if I detach the intake hose from the air filter box while the car is running.
I was beginning to suspect some camshaft lobe wear as per this post over on myturbodiesel.com (I know...don't beat me up over going there). I took off the valve cover this evening to check the camshaft and found that the valve lobes (not the lobes for the fuel injector rockers) were all worn to the extent that the chamfer at the lobe tip was gone and there were sharp edges. Two of the lobes were visibly round from one edge to the other when viewed straight on very similar to the pic below (I couldn't get pics of mine because it was too dark).