The IP does have alignment marks but you then need to fine tune the adjustment (most people here seem to do the drip test =>
PeachPartsWiki: How to Set IP Timing via the Drip Tube Method)
There's also information for the timing chain elongation measurement is here
PeachPartsWiki: Measuring Timing Chain Stretch
If you are used to rebuilding old US petrol engines (or even old English ones too!) then you might want to pay a little bit more attention to the specifications on this German diesel - I don't want to seem rude but they tend to have closer tolerances which are a bit more critical than you might think (if you are used to the other stuff).
It sounds like you have access to a machine shop - in which case I'd consider replacing the bore liners - re-boring to you existing piston sizes and getting it done now. I can't tell for sure (I don't think anyone can) but it sounds like you'll have it in bits again quite soon if you don't get it sorted now. This is just my gut feeling from information typed in a thread on the internet...