Yes, metal shims were used under the radiator, in addition to rubber pad/pads. Those shims would assist in obtaining proper front sheet metal alignment.
Many people use the short-shaft water pump successfully. My guess is that if the block is internally clean, and coolant flows freely throughout the block/head, you will have no problems. However, many people think that using a water pump relocation plate is the ideal configuration, since it places the water pump in the correct orientation to the radiator.
