Pamela, I have seen just about all of the photographs of the MENDOTA, but I am also aware that one of the photos that is often identified as the MENDOTA, is actually the USS AGAWAM, and there is one main point that shows the difference of both these vessels, that is easily seen, and that is the steam pipe on the MENDOTA, which is not on the AGAWAM. Also, there is another photo of a large part of the crew of the MIAMI which is often identified as the MENDOTA. I believe that all of the photographs of the MENDOTA were taken on the same day, and by Andrew J. Russell. In Russell's album he has two of these photographs, and identified the date in July, 1864, when they were taken. I assume you already know about this fact?
Was your great grandfather one of the officers on the vessel or one of the enlisted personnel? The officers are often easier to identify than the enlisted sailors, as their rank insignia can often be made out.
I will be glad to exchange notes on the photos, if you wish to do so.