Hi Helena,
Traveling 6 weeks in Peru and Colombia is no problem if you consider taking a flight from Lima to Bogota. Traveling overland will not only take quite some time (Ecuador lies between the 2 countries) you'll also be rushing to get to your destination.
Villa de Leyva is a wonderful colonial town not too far from Bogota. The main square there is the biggest in South America. There is an exhibition of a pliosauro fossil nearby. They've only found two of them in the world. One was found in Australia and is now in the Harvard University (USA) and the second one is, of course, in Villa de Leyva.
Cali is a very popular destination in Colombia. It's the capital of Salsa (music). The Cali nightlife scene should not be missed if you're there.
Another possibility is to travel in Peru and Bolivia, they're neighboring countries.
Lake Titicaca lies on the border of Peru and Bolivia. All major highlights such as
Cuzco,
Machu Picchu,
Arequipa and Lake Titicaca lie in Southern Peru.