Hi Jakbeau, When I visited Cuenca (it was in October), the first impression when I was on my own (I mean after landing, trip by taxi to the hotel) for a strol in the city, was tat I wasn't breathing easily. I noticed that being comparable with climbing the similar altituds in other mountains. It passed in an hour or two. Did your doctor recomend any aids for high altitude situations? The best way to find out is to go somewhere you have comparable heights. I think that this link might tell you more: hikingdude.com/hiking-high-altitude.shtml
Nicholas has a good idea about visiting somewhere closer to home with a similar altitude as here. I wouldn't personally recommend moving to Cuenca to anyone with COPD, obesity, or other health conditions that adversely effect breathing. Our thin air, many hills & steps, and pedestrian lifestyle just aren't a good fit.
I'm not worried about steps, hills, or a pedestrian life style, having lived in San Francisco for more than 15 years. I do worry about 8,000 feet of elevation on a daily basis, though. I hope to hear from other ex-pats who may have had breathing problems, if they have, and how they dealt with it.
Once you have been here for a while you shouldn't have any problems ever. I dont even thing about the altitude and when I got here it did make me sick for a week or two mixed with the new foods. but it not a problem normally. CHECK WITH YOUR DOCTOR! as far as I know you normally can put yourself in danger over more than 3000m-3500m. We are not that high in are comparison with so many other cities in the world. remember Altitude sickness and problems relating to Altitude are related to your genetic disposition and not related to fitness. but i don't know anything about your condition unfortunately and you as a person. once a person is here for more than 1 month they will not feel tired or out of breathe. and after 3 months they will forget about it completely and it will not affect them at all. But always if you are exercising at higher altitudes you will breath more.