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.