I paid just over $85 dollars for my water pump (the high mount pre 56 type) from the local NAPA.
Problem is with RockAuto they will tag you for shipping.. which puts it right up there with locally bought. Plus if the water pump is wrong, for whatever reason, taking it back to NAPA doesn't involve shipping

There really isn't much to a water pump. It either spins or leaks or just plain works. The only issue I can think of with a pump is if you altered the pulley ratios and are spinning it way to fast... so it just cavitates and doesn't move water.
Have you reverse flushed the new radiator to clean out the rust that was in the engine?