One of the tricks that I used was to finish the scarfs with a pad sander. When you notice the pattern of the filler core wood on the scarf is wavy, this is an indication that the thickness of the scarf is wavy (or uneven) By using a pad sander I was able to slowly fine tune the scarf. Sanding the areas where the core curved toward the scarf edge would gradually bring them up as the wood (scarf) got thinner. This all took minutes and I was able to get my core pattern nice and straight. You also have to remember that you're using thickned epoxy which will fill minor irregularities.

I also think stacking the panels is easier than doing an individual piece. It makes the scarfs all the same length. In a stack you can also sand them a bit with a block of wood and some 100 grit to fine tune them.