We had the same question regarding the distribution of our protein of interest. In our case we were interested in the distribution relative to another marker (in this case Synaptophysin as a general SV marker). We determined the ratio of staining intensities in the region of interest, thereby circumventing the problem of inherent staining variability. If this could be something you are interested in as well I'd be happy to explain our method to you in more detail!
It sounds very interesting. I would like to have advantage of your experience with the assay. Could you please provide me wih more details about your method.