Dont use any marks on the block, on the timing end for comparrison, use (if it has one) the mark on the flywheel and the inspection hole. 1 or 2 degrees wont make any difference as the timing can move back on these engine slightly on the tensioner once ran and if the timing is out it'll throw up a cam sensor fault. As for water pump failure - this is still common throughout the VW range and does not just affect 1.8t engines, the job to replace them is as you have already done plus removing the 3 bolts that hold the pump in place and swapping with new.
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I should need more convincing before redoing it, bearing in mind that altho' the cam(s) may be out (don't know which way or how mutch and German logic is sometimes counter intuitive) the injection is still "fired" independently you really need someone like Majesty78 /RUB87/or Theo who have put in zillions of hours I know majesty has been on here try a Pm