Seems to be some confusion on feet and inches (' vs.") in you post. I assume the well is 58 feet deep (I've heard of shallow wells, but 58" is the shallowest I've heard of ! LOL). So is the pump 3 inches or 3 feet off the bottom? 3 inches is too close, and you will keep stirring up sediment. But it should clear out eventually if its 3 feet.
You may want to let it set a week or so, to let the silt settle out.
What's the static height of the water column in the well (ie, if you leave it alone, how far down to the top of the water)?