In case anyone needs to have their fingerprints taken, it can be done at a police station out by the airport just off of Avenida Espana. See the address at the bottom of this post. I was not charged for the service. The form you need is FD-258 - fbi.gov/about-us/cjis/background-checks/standard-fingerprint-form-fd-258. While I had the forms mailed to me from the states, supposedly you can download them and print them out using the link I provided above.
I should mention that we sort of got the runaround at first, since the help desk had no idea that we could get our fingerprints taken there. They sent us to a different police station of Criminalistica which is out on the west side of Cuenca, who then sent us back over to the office by the airport. We eventually ended up in some small building located behind the main office, where we had our fingerprints taken. Supposedly the office of Crimanlistica on the west side will eventually house the personnel for fingerprinting, so keep that in mind.
Finally, I would like to mention that I hired Vicente Villafuerte who sometimes provides advise on this blog under the name Vinny66 to drive me to the Police department and to help with the translation. I recommend him to expats needing assistance with problem solving, transportation, shipping, or translation.
Departamento de Criminalistica de la Policia Nacional del Ecuador
Adress: Av. Gil Ramirez Davalos y Elia Liut, Cuenca