It's not completely clear from your description whether the defects show up only in the viewfinder image or in the film image. Any dust in the lens would likely be so out of focus that it would not show up as such on the negative in most cases; enough dust might, however, cause a general degradation of the image. Dust on the mirror or the pentaprism would not affect the film image. It sounds as if the problem is still in the viewing system. Can the eyepiece be removed and cleaned?