If your fresh water pump vains were damaged before rebuild you may have rubber pieces blocking the heat exchanger tubes.
How do you know you are lousing prime? If you are saying no water comes out the exaust when the motor is running, Then either the thru hull intake valve is closed, or the fresh water pump is bad or the power belt is loose or broke or the heat exchanger is clogged. Or your exaust elbow is cloged.
I would look at the heatexchanger and the exaust elbow. Unless you have other info