That looks great! I really enjoy it when i walk into a store and see a display that doesn't look commercially made. It seems like that's becoming more and more rare though. I guess i also don't go to stores that often either
The best way is to flatten with a wide diamond stone. A three inch wide coarse or extra coarse diamond stone costs $50-$60 and is used to establish or correct blade bevels before honing on the water stones so is very useful anyway if you are buying used tools. Or you can buy a Norton flattening stone for <$30, they are made of very coarse hard carbide and will stay reference flat for a long time. The cheapskate method is using a sheet of the coarsest wet sandpaper you can find on a sheet of flat ground glass. If you can't find a piece of flat glass, use melemine coated shelving, it's usually very flat and is what Frank Klaus uses in his sharpening video.
It helps if you develop a method of sharpening that minimizes uneven wear on the water stone. I use a guide and rub 50 strokes from stone center to just off the far edge, then rotate the stone 180 degrees and repeat. I'm trying to avoid the overused spot in the exact center of the stone. Get a small Nagura stone and rub around the edges when you start. That cuts down the high spots and develops an initial grit slurry which speeds things up.