Matt, That has come out really nice. I know you see only the "flaws", but trust me, a person who didn't make the knife will only see a stunning knife. BTW, you really aligned the grin well and got perfect concentricity in the grain rings on the handle aligning with the blade, as shown in the last photo.
Those "smear" places regularly show up in dyed and stabilized wood. It is places in the grain and such where the wood is denser, and takes the dye different ( or not at all). Because of the alignment of the grain that is most attractive for a knife and the flatter surface of the sides, they show more on the handle sides.
The flecks of white are often caused by buffing or sanding in the wood dust and/or polishing compound when finishing. In other cases, it is the lignin and dried sap/rosin. or other things in the wood grain, that does not dye and remains lighter color..... which shows up as flecks and speckles. Sealing the wood before the last couple grits in sanding may help, but in any wood dyed a darker shade, it is hard to avoid. Buffing very lightly with very little polish on the wheel helps. (On lighter woods, it sometimes shows up as dark flecks in the wood for the same reasons.) I actually like the white flecks on many handles. Sort of reminds me of the silver back look of an old bear.