Are there any structural differences in leishmania parasites that allows some species affinity to infect cutaneous tissues and others the spleen and liver?
Its hard to say, the different Leishmania species show different proteins profiles during the infection and dissemination stage, in addition to the wide genetic and inmunologic background of the infected people. There are some evidence about it, the pacient inmunologic status its important to determine the tissular tropism of Leishmania or severity of the infection. In inmunocompromised pacients even a non-pathogenic trypanosomatid parasite can generate a disease http://www.who.int/leishmaniasis/burden/hiv_coinfection/en/ATMP7.pdf. The antigenic and pathogenic determinants are not fully known yet, please read this for an approximation http://www.kinetoplastids.com/content/1/1/1. Because the distribution of Leishmania is limited for the presence of competent vectors and how the geographic and ecological barriers affect them, also you have to consider the rol of the insect (saliva) as another important factor in how different species of Leishmania can have different levels of pathogenicity and tropism. This is a wide topic in research yet.
I agreed with previous answer of Dr. Paternina and I would love to share the following:
"Some investigators illustrated that there are a few genes influenced the tissue-specific expression of disease associated with different Leishmania species".and you can see the following paper
Peacock, C. S., Seeger, K., Harris, D., Murphy, L., Ruiz, J. C., Quail, M. A., ... & Berriman, M. (2007). Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nature genetics, 39(7), 839-847.