Just finished my first layered map project - 50 x 50 cm

I did a layered terrain piece of the hills behind my parents' place last year, 40 by 40, and hit exactly the same wall with the paint. On birch ply the grain soaks up color unevenly no matter how much you sand, so sanding alone never fully fixed it for me. What actually worked was sealing the surface first. I wiped a coat of watered-down wood glue over each layer, let it dry, gave it a light sand with 240 grit, then painted. The grain still shows a bit if you look close, but the finish went from blotchy to even.

Another trick if you want the paint to sit flatter: a coat of cheap gesso or primer tinted toward your final color, then the topcoat on top. It felt like overkill on a plywood project but it made the labels pop because the background stopped fighting the ink. On the alignment side, I started with matches in the corner holes like you did with toothpicks, but on the bigger layers they were too flexible. Swapped to 4mm dowels cut into short stubs and the layers stopped creeping sideways while the glue cured. Also worth leaving the dowel holes just a hair loose so you can nudge a layer before it grabs.

If you do map number two, consider cutting a small hidden notch in one edge of each layer as well as the corner holes. It gives you a second reference so a layer can't rotate even slightly, which is hard to spot untill the whole stack is glued.

For the big terrain board I built last winter I stopped fighting the grain and just let it show. First attempt with ordinary acrylic went the same blotchy way you describe, so I stripped it back with a heat gun and some scraping, then wiped each finished layer with a light coat of walnut stain before assembly. The grain still reads through the color, but evenly, so it ends up looking like a deliberate wood-tone map instead of a botched paint job. Ran a clear matte sealer over the top once everything was glued and it's held up fine on the wall for a year now. On the stacking side, I did somthing similar to your corner holes but went with short lengths of 3mm dowel instead of toothpicks, tapped in tight and glued permanently. Once the stack is done you can sand the dowel ends flush with the surface and they vanish completely. On a piece that size I'd worry a toothpick would flex too much across three or four layers of buildup, but maybe yours were short enough that it didn't matter.

If you do want solid opaque color on the next one, spray might suit you better than brushing. A couple of thin passes builds up without dragging the grain around the way a brush does.

I tried one of these stacked maps with my kid for a school thing, way smaller, maybe 20 cm across, and the pieces started curling on us after a few days. The thin sheets just wouldn't sit flat, and the whole thing ended up wobbly like a warped pancake. Does yours stay flat at that size, or did you have to weigh the layers down with books while the glue dried? Also curious how long you left it before painting, since I rushed that part and the color never looked right.

Quick update—I finally solved the paint issue. I listened to the advice about surface prep. Instead of just sanding the layers, I sealed everything first before applying the color coat. That made a huge difference and the plywood grain stopped showing through as much as it did before. It looks much smoother now!