Can’t be 3/8” casing. Has to be 4” or larger. The water in the pipes can get dirty sitting unused, but it shouldn’t be that bad from the well. It is hard to clean up a well that only makes 1.3 GPM. You may have to pump it out dozens or more times, which takes days. A water test would also be a good idea. Find out what it is your trying to clean out. You might have to treat the well to get it to clean up.