Do not waste your time and money pulling that head. You are likely to do more harm tahn good.
A) The damage will not be visible to the naked eye before catastrophic failure. The reason for the failure is repeated grain structure change, until the whole piston fails in one occurence. I doubt even X-rays will detect problems unless they are really pretty close to happening.
B) Factory engines are built under laboratory conditions. Everything must be spotless. I have not seen a local workshop that works cleanly enough (I am not saying they don't exist, but I have not seen one). And I have not seen a commercially-rebuilt engine that has lasted as long as a factory original.
C) If you pull an engine apart, do not even consider putting it back together without replacing the head gasket and oil pump. If you replace the pistons, you need to replace the rings. If you replace the rings, you need to hone the bores. If you hone the bores, you need to strip everything down, clean everything meticulously. By the time you do this, it's effectively a complete rebuild.
1) First (and without touching anything else) fit a madman. Drive it for a while like that, and drive it as hard as you ever have. This will soon give you an idea of what the EGT's have been doing.
2) If you find that it is likely your EGT's have gone too high, try the borescope (which I believe will tell you nothing but might make you feel better), and have an oil analysis done (probably only of slightly more value).
3) If you are still not happy, trade it on a 4.8.
And here lies my issue with the 3l TDI: most guys who drive them spend almost as much money at the doctor having ulcers and stress-related problems treated as the guys with the 4.8's spend at the pumps (ok, not really, but most of them spend a lot of time stressing).
Mag ons ons kenniskry met lekkerkry aanhoukry.