The 360 km Ecuador to Peru bus trip was the ride we were dreading because we had read about all the difficulties experienced along this route. The typical stories included getting on a bus that only took them to the nearest border town, but had to find a taxi to actually take them to the Ecuadorian immigration office (which is 3 km away from the actual border), then had to find a taxi or walk across the border to the Peruvian immigration office (which is also another 3 km away from the actual border in the town of Zarumilla), then had to locate another bus that continued down into Peru. Also, some have reported getting a bus from Ecuador that takes them across the Peruvian border, but did not stop at the Ecuadorian immigration office to get stamped out, so they had to return to Ecuador. Not to mention the multiple scam artists who prey on tourists trying to do this border crossing on their own. It all sounded very complicated so we were not looking forward to this experience. The most important point for us to recognize was that no matter how much research and planning we did, each person experienced a different twist or turn. The best information we found was through the Cuenca expat website called www.GoGo-Gringo.com. We took their recommendations, but as imagined, our experience did not exactly match what they went through. Here is the documentation of OUR Cuenca to Máncora trip in hopes that this will add to the body of information available to alleviate some uncertainty for the next soul thinking about making this trip.
Our plan was to leave Cuenca, Ecuador on Wednesday, June 20th, 2012.
Monday, June 18th: We took a taxi to the main Terminal Terrestre in Cuenca to purchase tickets for our anticipated bus ride to Máncora, Peru. GoGo-Gringo recommended buying tickets through the Pullman Sucre bus line all the way to Máncora, because this bus was suppose to take us directly to the Ecuadorian immigration; then transfer us to the CIFA bus line at the border town of Huaquillas, Ecuador; which will then take us through the Peruvian immigration and onto our destination. We saw on the bus schedule that there was a 9 am bus to Máncora that GoGo-Gringo also took, but when we talked to the attendant at the window, we only had 2 choices: 7:15 am or 9 pm bus. They should really change the posted bus schedule if it's not accurate...but, whatever. Yet another reason to go a day or two in advance to purchase tickets. We went with the 7:15 am departure because we certainly did not want to risk the dangers of traveling overnight. We were given 2 separate tickets. One from Cuenca to Huaquillas at $7/pp and another from Huaquillas to Máncora at $8/pp.
Wednesday, June 20th, 0700: To get from the inside of the terminal to the outside where the buses are lined up, it costs 10 cents to go through the turnstile. Be warned, once you go through the turnstile, there really is no way to get back into the terminal which has the restrooms, food, etc.
0715: We located the one and only Pullman Sucre bus among about a dozen buses idling, but we started getting worried when the bus door was still closed, there was no bus driver or bus attendant that usually accompanies the ride, and no overt signage that says this bus was headed towards Huaquillas. Miraculously, the bus personnel and passengers showed up at 0720, we all got onboard and the bus pulled away a couple of minutes later. We had assigned seats on this bus.
0740: We meandered through Cuenca, stopping a million times to pick up passengers until the bus was full. We were finally getting used to this process! We picked up a bunch of people at Centro Comercial El Arenal - a HUGE indoor and outdoor central market of Cuenca. It looked like an excellent place for sightseeing...next time we're in town.
0800: We were finally headed out of Cuenca, southwest bound towards Santa Rosa, Machala, and Huaquillas.
0930: This ride was rough at times. Literally, dirt roads through the steep mountains! We hypothesized that the bus attendant started playing a video on board (Rambo, First Blood at that!) so that we would be distracted from the sheer vertical drops along our route.
1000: As we started leaving the Andes behind, the landscape changed dramatically to dry, arrid, rocky, brown mountains with a river running through it. It was very beautiful.
1045: We pulled into the very dusty, depressed town of Machala at an actual Pullman Sucre bus station....and to think we were at one point, thinking about spending the night here to break up the 10-hour bus ride.
1100: We started seeing HUGE banana groves to the horizon on both sides. Ecuador is one of the biggest banana exporters in the world, and we witnessed where they all come from. Wow!
1130: We briefly stopped in the city of Santa Rosa. Also, very dusty and run-down.
1200: ...then, the city of Arenillas. Ditto on the conditions of this town...
1230: We finally made it to the Huaquillas CIFA bus terminal where we were...unexpectedly...dropped off. It was unexpected because in all our research, we were suppose to pass through the Ecuadorian immigration office BEFORE we got dropped off in Huaquillas! Arrghhh. Of course, trying to have this conversation with the bus attendant and CIFA office lady was fruitless. Great. We had no idea where the Ecuadorian immigration office was, nor did we know when our CIFA bus towards Máncora was leaving. In the waiting area, we met 2 backpackers who were headed to Piura - a city 3 hours past Máncora. They said our bus would not be leaving until 2:30 pm (2 hours later), which was confirmed by 2 other CIFA bus personnel. By the way, none of the posted schedules said anything about Máncora or 2:30 pm - double "great." After using the nice restrooms at the bus stop for 20 cents, we tried to make good use of our time, so we headed across the street to grab some lunch.
1245: While we were finishing up our lunch (chicken, lentils, rice) Mike saw our backpacker buddies getting onto a bus that just pulled in alongside the street, but not into the actual bus station. Akiko ran across the street to the bus, confirming that it was headed to Piura (which means it will also go through Máncora), so we quickly paid for our lunch half-eaten, and jumped on this bus. We probably could've waited for the Máncora-bound bus (assuming it was still on its way at 2:30 pm), but this was even better since we didn't have to kill 2 hours at the bus station. It was a leap of faith, since the only destination signage on the bus was "Directo." It didn't say Piura anywhere, but the bus attendant saw our CIFA tickets and told us to get on...so, that was that. The only other concern at this point was getting to the Ecuadorian immigration office before we headed into Peru.1300: Lo and behold, we pulled into a brand new Ecuador immigration complex! Whew. All the blogs mentioned a run-down immigration building, so with the new facility, perhaps the bus process also changed recently. Either way, we were very glad to see that things were working out after all. We filled out an immigration card and waited in line to get stamped out of Ecuador. 20 minutes later, we were back on the same bus, headed towards Peru.
1330: The bus drove around a crazy busy market and bridge that spans the river separating Ecuador and Peru.
1345: We then arrived at the Peruvian immigration office in Zarumilla where we got off the bus again to get stamped-in to Peru. Again, 20 minutes later, we were back on the same bus, headed towards Máncora. Things were looking good at this point!
1430: We rolled into an actual CIFA bus terminal in Tumbes to get the windows washed and for a restroom break.
1500: We were pleased that we were passing through all these little coastal towns without stopping. Perhaps the "Directo" on the bus actually meant something. We could feel the heat of the desert sun, with our only "air conditioning" being the windows wide open, smelling all the smells that rural Peru had to offer. We saw lots of farmland and desert, but we were finally rewarded with a view of the ocean! Yay!
1545: We bypassed Punta Sol, knowing Máncora was the next town.
1600: It had been a really long day, so when we had to go through a Cargo/Baggage Inspection station in the middle of nowhere, we were not happy. They actually made us get off of the bus and go through customs.
1620: 20 minutes later, we confirmed with the bus attendant that we wanted off in Máncora and we were finally (hopefully) headed there.
1630: The bus attendant flagged us to get ready to jump off the bus as we approach Máncora, and with barely a stop, we jumped off the bus to an assault of mototaxi drivers and salespeople for all the various hotels and tourist services.
1630: Although we got off in Máncora, we still had another 15 km to our final destination of Los Organos beach. After walking through Máncora for a few minutes to gain our bearings, we didn't see any taxis so we paid 30 soles (~$10, too much probably but we didn't care at this point!) for a mototaxi to take us to our lodging. Apparently, there are no official taxis; however, many people ride-share for approximately 2.50 soles/pp if the car has 5 passengers; or, you can hire the whole car for 12 soles. The mototaxi was okay, but obviously took longer to get to Los Organos than a car; not to mention we literally thought we would have to get out and push this thing over a few hills that it was sputtering hard to overcome. 
1700: We finally arrived at our oasis in Los Organos, 10 hours later.
So, this was yet another adventure that overall, went as well as we could expect. Not knowing what to expect next all along the way is mentally exhausting, but we remained positive the whole trip. We won't go out on a limb and say we enjoyed it, but we gained more confidence and we would do it all over again.