The first color adjustment is the touch-up work to all the putty marks. Simply "paint" on the background to blend with the rest of the surrounding wood colors. It does not have to be a perfect match but it must blend. You need smooth natural looking color transitions. Apply a few different shades and color variations on large area touch-ups. Real wood has many color changes. Your hand painted wood should have them too. The finished look should not be a one color paint job.