Is your fuel line that passes from the pump to the carburetor touching the water pump anywhere? If so bend it so that it doesn't. Keep it off of the water passage in the intake also.
Are there fuel stains on the carburetor indicating a slow leak from the float bowl? I guess it would actually leak into the intake if the well plugs were leaking.
I use a glass filter without any issues. I want to see debris if any should ever get in there.