I would first check that you actually have water passing through the intake through hull and into the inlet line. Disconnect the inlet hose from the through hull, after ensuring that the sea cock is in the closed position. Carefully open the sea cock slightly to allow a small stream of water to pass through the semi-open sea cock. If you have a small stream of water present, briefly open the sea cock fully and ensure that you have a strong, steady flow of water. Close the sea cock immediately!
If no water streams into the boat when the sea cock is slightly open, try carefully opening it all the way. If no water stream is present when fully open, you might want to try poking something stiff but flexible through the sea cock to dislodge whatever might be blocking the inlet (i.e. nasty growth of some description, jellyfish, small eel, etc.). Be careful. If something is dislodged with this method, water may start to rush through the sea cock. Remove your poking stick and close the sea cock immediately!
Assuming you have water flow through the sea cock, ensure that the inlet hose is clear through to the pump. If it is and still you can't get any water into the bowl, you are probably in need of a pump overhaul. For the PHII you can buy the overhaul kit of o-rings, balls, gaskets, flappers, and joker valve or you can get a completely new pump assembly. The assembly is pricey, but is easy to install and has the upside of updating your toilet to the latest version. We installed the pump assembly 3 years ago, and I just put the overhaul kit in it again this last weekend. I was impressed how clean it all was inside! Even the factory grease was still present. This overhaul was simply a preventive maintenance measure for us. We have written before about our routine of pouring 1 gallon of vinegar into the head, once a month and letting it soak in the toilet, pump and hoses for a few hours before pumping it out. It was nice to see first hand that this method is keeping everything in good condition inside.
