When we decided to re-do the website we opted to go without the bus maps. In the previous system we used it required continuous updates and a great deal of man power. It wasn’t in the cards given all of the ongoing changes to the transit system and the need to hire a full time employee just to keep the bus routes in order. Shortly after we came out with our bus route application several other versions came to the scene. My recommendation would be to get in touch with Christopher King who operates the Cuenca Bus Sherpa http://www.cuencabussherpa.com They have all of the current routes mapped out in print and online.
Hope that helps!