I think the “smear” effect is due to the opposing grains of a typical plywood glue-up. Typically, in a 5 layer glue-up, two of the layers will be opposing grain. Not that it’s a bad idea, but rather than going to the trouble of cutting out ever smaller pieces and gluing them together, you might try gluing all the pieces of your veneer with all the wood grain perpendicular to the bottom of the board. This way, with the grain all running the same direction, foiling is simplifed, and you can measure your cuts to even your foil. Of course, you could do that on any fin layup that has different colored layers.
The allignment marks thing is pretty much how I foiled the second fin. The first one I just foiled it how I thought I wanted it. then I placed it opposite of the other fin and marked out with pencil where the layering was and just matched it with the same techniques I used to foil the first fin. It was all done by hand with a surform blade that I cut and grinded for use specifically on wood fins, and I used 50, 80, 150, 220, and 400 paper with blocks and a 4" cardboard cylinder to get to the final product.
The wood used was 1/2" Baltic Birch ply ripped and planed down to roughly the same thickness as the solid Spruce burl piece (slightly over 1/4" in thickness), then the inside “keel” shape was cut out of the ply on a scroll saw (1/2 off at Harbor Freight last week by the way), and then I traced that cut out onto the spruce burl. These pieces were cut to fit as perfectly as I could get them, and then glued with Gorilla glue and any bubbleouts were filled in with a mixture of tightbond II and Elmers wood filled wood glue (mistake…had to be completely sanded off because it only cured on the outside and when I sanded through the glue it just heated up and became goo on my paper).