Hey everybody! Hubby and I went to Guayaquil yesterday for his medical, and luckily everything went just fine. Before going to the medical, I had a few doubts/questions, and upon searching here on VJ for relevant information, I found nothing! Apparently nobody has really gone into detail about how this part of the process goes, so I figured I'd post a step-by-step review on how it went to help future Ecua-filers. There were a few things that would have been helpful to us had we known before going, so hopefully this will do that for someone else!
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Hubby and I live in Bahia, Manabi, so we're a good 5 - 6 hours away from Guayaquil. There are only three board certified doctors in all of Ecuador that can do the medical - two in Quito, and one in Guayaquil. Since we're closer to Guayas than Pichincha, the choice between the three was pretty simple. We called the doctor's office (number can be found here: http://guayaquil.usconsulate.gov/medical_exam2.html) the day after we got the P4 email from NVC to make the appointment. Please note - you can only make the medical appointment AFTER you already have an interview scheduled! The lady we spoke to on the phone said the medical date should be at least ten days before the interview date, but made ours a bit earlier - our interview is on May 29th, and the medical appointment was scheduled for May 16th. She read off a list of things we had to bring (hubby's passport with a color photocopy, three photos carnet sized (NOT passport size!), a copy of the P4 email, and any vaccination records hubby had along with a photocopy), and told us to be at the office by 8 AM on the day of.
Since we had to be there early on the 16th and we live so far away, hubby and I had to take a bus at 11:30 PM the night before. We got to the bus terminal in Guayaquil at 4 AM, sat around for three hours, and grabbed a taxi to the address we'd gotten off the consulate website. The office itself is right next to the Vélez/Boyacá intersection - it's got a big gold colored set of bars with a guard outside and a lady sitting on the other side behind a desk. We explained that we had an appointment to the lady, who opened the gate for us and told us to go up to the second floor. We took the elevator (which felt like it was going to collapse under us) and found a small floor with three doors. The one on the left was the only one that looked to be open for business, so we went in, took a number, and sat down with about ten other people in the waiting room.
After about ten minutes, our number got called so we went over to the secretary's desk and turned over the requirements she'd asked for over the phone. She took them all, and gave hubby two papers to fill out. After he was done, she gave him a paper and told us to go to the Clínica Panamericana, near the Panama/Roca interesection, to get a chest x-ray. She also gave him a separate piece of paper and told him to go to the adjacent room to pay the 140$ for the consult. Afterwards she said to wait for the doctor to call his name so she could take some blood. We paid, waited for his turn to get his blood taken, and then went to the clinic.
The clinic itself was very straightforward - went in, gave the secretary the paper, and waited for his name to be called. It took about twenty minutes for his turn, but only about five for the actual x-ray. After that we went back to the original doctor's office, and sat down to wait again. This time, a different girl called hubby's name, and we went over to her cubicle. She asked hubby who was petitioning for his visa, and he said me. She told us that our vaccination records were good, but that we were missing the influenza shot and would have to pay to have it done there. I explained to her that we'd gone to three different health centers to get that shot, but everyone had told us that since flu season was over it wasn't being given out anymore. She said that this was true, but that in certain places in Guayaquil it could still be given, and was thus still required. He was also missing his mumps vaccine, but since he had already had mumps as a kid, he wouldn't have to pay for that one. We paid the 15$ for the flu shot, and sat back down in the waiting room for his name to be called for the physical and shot.
Please note - while we were lucky enough to only have to pay for one shot, there were other people there who had come unprepared and had to pay for four or five, each one costing at least 10$. We asked the doctor, and he said you could pay up to 95$ in vaccines if you didn't bring any records at all, so try to get your vaccines done for free in public hospitals before the medical! Much cheaper, and less painful - imagine getting five shots done at once? Yuck. 
We waited at least half an hour for his name to be called. When it finally was, he took the receipt from having paid for the flu shot and went into the exam room while I waited in the waiting room. It was very quick - maybe ten minutes - and he came back out with a band-aid on his arm and his shoes in hand. They asked some basic questions (which I'll list in a moment), did an eye exam, checked his height and weight, and made him strip down to his underwear to check his "privates" (I'm assuming to make sure he had no VDs). He didn't do a hearing test - we'd been a little worried about that, because hubby is deaf in one ear, but the doctor didn't even ask about it! Afterwards hubby got dressed, and the doctor told him to come back at 4 PM to pick up his x-ray and sealed envelope, which we did with no problem.
We got to the office at around 7:45, and were completely done by 11:30. If you don't live in Guayaquil, make sure you have something to do for a few hours afterwards, because the blood work doesn't come back until 4 PM. Luckily we had some other things to do, so it was okay - but there was another older lady who had to sit in the waiting room for all that time!
Also, make sure you bring at least 200$ with you. The consult itself costs 140$, but like I said the vaccines are expensive, and they send you around the city so you have to pay for taxis. We only spent like 20$ in taxis, but still, you're better off safe than sorry. 
Questions hubby was asked:
1. Do you use drugs?
2. Do you have any venereal diseases?
3. Have you ever had any surgeries?
4. Do you smoke?
5. Do you have problems with alcohol?
6. Do you have asthma?
If hubby remembers any others, I'll edit the post to add them, but he said they were very basic questions and very easy to answer. Also, he said when the doctor asked if he'd had any surgeries, hubby said "Yes, one on my elbow when I broke it as a kid", and the doctor said "Are you sure you've never had sebaceous cysts?" Hubby said no, because he hasn't, but I thought it was odd the doctor would ask about such a specific condition. Maybe he was trying to confuse hubby with a trick question? Not sure. 
Hopefully this was helpful to someone, and lots of luck in your medicals!