The knocking sound you hear may be pre-ignition which is not good. Either the motor is too hot, poor quality gas, the timing is too far advanced, or the motor is running too lean.
Blocked water passages can cause the motor to run hot. If you found a lot of salt and sand in and around the thermostat housing, I would be concerned about the water passages in the exhaust cover. They're smaller and are more easily clogged by saltwater corrosion, and sand. The biggest problem with checking the exhaust cover is the 1/4 X 20 threaded bolts that hold it on have a tendency to break when you are removing them. If you decide to do this, be sure you have access to good quality drill bits (Cobalt steel) and a 1/4 X 20 tap or possibly a heli-coil repair kit and some patience. I would check the timing and fuel mixture first before I would check the exhaust cover because they are easier to do and less of a chance of causing a problem.
The timing is easily checked with a timing light.
Make sure that the idle mixture screws are set no less than 1 turn out from lightly seated all the way in. Typically 1-1/8 turn to 1-1/4 turn out from lightly seated will get you in the ball park. Each motor is slightly different. Have you changed the fuel pump diaphragm?
Blocked water passages can cause the motor to run hot. If you found a lot of salt and sand in and around the thermostat housing, I would be concerned about the water passages in the exhaust cover. They're smaller and are more easily clogged by saltwater corrosion, and sand. The biggest problem with checking the exhaust cover is the 1/4 X 20 threaded bolts that hold it on have a tendency to break when you are removing them. If you decide to do this, be sure you have access to good quality drill bits (Cobalt steel) and a 1/4 X 20 tap or possibly a heli-coil repair kit and some patience. I would check the timing and fuel mixture first before I would check the exhaust cover because they are easier to do and less of a chance of causing a problem.
The timing is easily checked with a timing light.
Make sure that the idle mixture screws are set no less than 1 turn out from lightly seated all the way in. Typically 1-1/8 turn to 1-1/4 turn out from lightly seated will get you in the ball park. Each motor is slightly different. Have you changed the fuel pump diaphragm?