You can make a fill for those cracks by mixing up some epoxy and some of the sanding dust from the scales. They look too deep to sand out without losing a lot of material. Given the tearout around the countersink holes and the pop of the grain, I would call this either a species that is more "splitty" or one that came from a much different climate zone than where the scales are or were stored. Once the cracks are patched and it's had another 800 grit sanding, try wiping it with mineral oil to see if it gets the shine you want and if the grain swells a bit more full. If that's the kind of look you want, then a coat of poly finish will replicate that effect, but test it in a small area first. The species looks like a "Desert Ironwood" I got off the shelf at Rockler one day, and if that's the case, then a finish in Boiled Linsee Oil will really help fill in the grain along the finger wells.
The scales don't look burned to me since the drill holes show some lighter wood even though it looks like the bits were dull judging by the level of polish and roughness. You could check by sanding the insides of the scales back to 60 grit and seeing if they change color appreciably. If nothing else, finishing these scales will be informative and good practice for the next time.
