Power steering pump replacement questions

The bolts that go through the water pump and timing cover do go into a water jacket, so, totally normal. The original bolts had a nylon insert in them that helped seal the threads. You can use some thread sealer instead to reuse your bolts. There were several different pumps and pulley combinations on Mopars. Some had press-on pulleys with a solid/plain end shaft, some with a hollow shaft with threads, and some with a external threads and a bolt-on pulley. If your is a plain end shaft, you need to use a special puller for the pulley and then have it pressed onto the new pump.