Water line about half way down on the pontoon is pretty common.
I don't see any need for that quick coupler on the engine if you don't have the need for it. Without that quick coupler, an on/off valve (located at that filter as a good mounting point) sounds like a good plan here, especially if you have gas disapperaing....
I have one of those gas tanks that fit down inside that engine pod, and I don't care for it at all on our 20' boat. Full, it's very heavy, and the back of the boat sits noticeably lower when full. It holds something like 25 gallons, which is enough gas for months the way the 50hp Honda uses it. 6 gallons would be more than enough, and MUCH easier to make sure the gas is staying fresh. Converting to a portable tank as we speak.