Is the water pump belt driven?
I am not sure about yoru specific model yanmar. On the YSM 12 there is only one seal and the side where the spring is exposed is on the same side where the water is.
For the oil, I use shell rotella 15-40 synthetic. If your engine hasn't been running on synthetic from the beginning don't put it in there though. It will start burning oil. The book says 10-20 degrees C-20/20W. 20-35 degrees C- 30 or 40 weight.