Started pulling things apart on the van last night. Doesn't look too good so far. I was hoping for an outside chance that the engine problems (rapping and thumping noises and a dead miss) could have been a collapsed hydraulic lifter, which sometimes happens to these, but all the lifters are fully pumped up and seem to be working fine.
One thing that is clear right away is that this engine has seen either a huge amount of heat in the cylinder head, or very poor routine maintenance, or both. The inside of the head is coated with black, slimy buildup from polymerized engine oil broken down by too infrequent changes or excess heat exposure from the aggressive state of tune. This does not give me much hope for the condition of the rest of the engine.
Here are some pictures so far, along with some other pictures for comparison to more healthy engines that have seen less abuse (another AHU TDI and my 745's D24T engine -- sadly showing my shattered camshaft from a couple years ago).
See the strong family resemblance between this TDI engine and the D24 engines. They knew they had a good basic design and no need to change it.
Going to pull the head off next and see what that looks like, hopefully later this week.