I think you can get what you want with some tweaking of your parameters. Put 18" or so of ground/dirt between your house wall and the pond edge. Use a liner as it's easier and faster. If going 2' above, I'd aim for 2' below. Goldfish (shubunkins is one type) would be better for 1000 gallons. If you want koi, think 1000 gallons for the first one and 250-500 for each additional. I think you mentioned wanting natural plant filteration, so that's a good idea in the form of a bog filter (actually, upflow wetland filter). Do some searching here for both ideas and directions and see if it's something you want to employ. If you do, you won't be sorry; many of us are using this form of filtration and enjoy all the time we NEVER have to clean pads, etc!
If you want the slate look, make your 'above ground' portion from ground contact 6x6s and affix the tile to the face for effect. The liner would go in, up the wall, over, and can be fastened to the top of the wood box, where you'd then put more tile as coping or another form of edging.
Putting the pond near but not ON the wall also gives you planting area to naturalize your pond, too.
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