sure you could pad between the liner and the wood, all you would do is epoxy a strip of rubber to the edge of the window, and melt the rubber and the liner together. If i were doing this though, i agree that concrete and rebar is much easier and probobly cheaper. Also, you add a "foundation" very easily, limiting the possibilty of a hurricane coming in and fliping the pond. In terms of filtration, if you wanted to put a small area behind the pond for a pump and a pond filter, that would be ideal. Another idea would be to use a big pond canister filter and rig it to a waterfall, so it looks nice and provides filtration. Just make sure that your tunring the water over enough and that the surface of the water is being broken, for gas exchange. Actually, having two pumps would be a better idea. Both pumps with a filter, and you could have one running up and into a waterfall.
One question i have is...wouldnt an arowana jump out to grab and insects it sees?