Answer: promastigotes of Leishmania species.
Thank you for everyone who wrote in with an answer for this case. Most of you recognized that this is the motile form (promastigote) of Leishmania, which grows in culture at 25C and is the stage found in the sandfly vector. As noted by anonymous, the faint big dark pink blob is the nucleus and the small clear pink dot is the kinetoplast:
The 'warty' appearance of the lesions was a bit atypical compared to the classic ulcerative leishmanial lesion, but the chronic nature of the lesions and history of travel to South America fit well with the diagnosis of leishmaniasis. I reviewed all of the skin biopsies from this case and *maybe* saw a few amastigotes, but the overall appearance was nothing like the classic histopathology that I am used to seeing. The dermatologists have hypothesized that the lack of amastigotes in the skin biopsies may be due to an unusual immune response associated with the proliferative warty nature of the lesions.
The CDC is currently performing PCR to speciate the organism, but based on the smaller size of the promastigotes in culture, think it is most likely to be L. braziliensis or L. (Viannia) panamensis. Both of these are agents of cutaneous and mucocutaneous leishmaniasis, so the patient will most likely be treated with a systemic therapy such as liposomal Amphotericin B or (more likely) the pentavalent antimonial Pentostam (sodium stibogluconate).