I emailed Moyer Marine with this problem and Don replied. I think it is amazing that he answers any time I have a question. Everyone go buy something from Moyer.
Anyway, he says that the water should always flow easily to the intake of the pump. That doesn't seem to be happening. I have a basket filter that when the top is opened, no water comes out even with the thru hull valve open. Maybe the first step is to lower this filter? I would have to close the thru hull to inspect the basket but that's no big deal.
He also says that an old impeller can wear the inside of the impeller section. Maybe that has happened to the point that the pump can't overcome the improperly placed filter?