From the palette, choose the background color to ink the speckles; this makes them transparent in the output (although they still show up in the Transparent color in your palette in draft display mode), allowing the color of the ink to show through. When you are using the inkbrush, the area of the circle shows you its size. If you need to ink small areas of detail, zoom in.
Ink over the blemishes. The Freehand Inkbrush tool only affects the trace lines, so there's no danger of inking into any of the paint regions.