I just did some re-plumbing on my unit to change the heather bypass and winterizing valves. During the checkout, the water pump wouldn't work without lots of air in the lines, the problem was traced to a loose clamp on the inlet to the water pump, it was trying to suck air along with the water. You might look for a loose clamp or fitting on the inlet to the pump, it didn't take much tightening of the clamp to fix the problem.
Dennis