There is one direct bus, operated by Azuay and departing Cuenca at 9:30PM. I went to the terminal the night before to buy the ticket for $15. I hear the day bus that was available last year no longer runs, but I am not sure about that.
The hardest part of the ride is filling out the immigration forms as the bus makes and shakes its way down the mountains from Cuenca. The bus does not require transferring at the border, but you do have to get out to get your papers. There is one building with two desks and two lines: one line to leave Ecuador, then the other line to enter Peru. Make sure to keep any papers they give (back) to you to show to get back on the bus. The bus makes a customs stop an hour after crossing the border. I don’t think any luggage was removed. It’s just a sit and wait affair unless they suspect something.
The bus got to Máncora shortly before 5 in the morning and stopped on the Panamericana. Moto drivers swarm to pick up the passengers. They jack up the price and it’s difficult to argue for a fair one at this point, especially with no Peruvian Nuevos Soles on hand. Normally, it shouldn’t cost any more than 6 soles to get anywhere in Máncora.
Retrospective
Update: Moved to new category “Travel Logisitics” for posts that may be useful to some people but are not terribly interesting if you don’t need the info.