As said it´s difficult to say what Ruta 40 will be like in a few weeks let alone several months. We rode it back in January and it is quite a challenge, the stretch for 50 km north of Tres Largo being the worst section, we met a rider who had fallen twice on that and by the time he got to Pertio Mereno he was looking for someone to rebuild the rear Ohlins. The road is a good width but you end up trying to ride in a foot wide trench with what feels like a 30 to 40 mph side wind.
The Carretera Austral, Chile, is narrower and also needs to be treated with care as there is more traffic.
The route you mention in Peru is Route 3. If you struggle on Ruta 40 and Carretera Austral think twice about the route 3 in Peru. I don´t think I would ride it 2 up and loaded. It is a truly fantastic ride and toughest but for us one of the high lights of this trip. We rode north to south, basicly Chachapoyas to Urubamba (Cuzco) and it took 12 days with one day off. It will test any rider and depending on weather, you could encounter almost every type of surface, and the highest pass was over 4700 metres, if anything happens to you or your bikes it could be serious. We left Chachapoyas, rode 140 miles in 10 hours (with stops) and traveled 47 miles as the crow flies, and there are lots of days like that.
You will need a good map and a GPS will be helpful as there are no road signs, the locals will help, if you can, try and get a set of maps from the Peru Automobile Association, not the best maps but they will help to show towns with hotels.

Columbia is a must do but like anywhere in south and central america be carefull. We took a sail boat around the Darien, check out the boat before you commit as there are some bad stories about some of the crossings and not all the boats are in the best of condition. Checkout the time of year to make this crossing as I think December to March is a time for high winds and heavy seas.

Steve